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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs765766910

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:1520332 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000057 (15/264690, TOPMED)
T=0.000007 (1/140298, GnomAD)
A=0.00004 (1/23038, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
IFT140 : Synonymous Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 23038 C=0.99996 A=0.00004, T=0.00000
European Sub 15752 C=0.99994 A=0.00006, T=0.00000
African Sub 3492 C=1.0000 A=0.0000, T=0.0000
African Others Sub 122 C=1.000 A=0.000, T=0.000
African American Sub 3370 C=1.0000 A=0.0000, T=0.0000
Asian Sub 168 C=1.000 A=0.000, T=0.000
East Asian Sub 112 C=1.000 A=0.000, T=0.000
Other Asian Sub 56 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 2772 C=1.0000 A=0.0000, T=0.0000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999943 T=0.000057
gnomAD - Genomes Global Study-wide 140298 C=0.999993 T=0.000007
gnomAD - Genomes European Sub 75962 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42060 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13664 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 23038 C=0.99996 A=0.00004, T=0.00000
Allele Frequency Aggregator European Sub 15752 C=0.99994 A=0.00006, T=0.00000
Allele Frequency Aggregator African Sub 3492 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 2772 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, T=0.00
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 16 NC_000016.10:g.1520332C>A
GRCh38.p14 chr 16 NC_000016.10:g.1520332C>T
GRCh37.p13 chr 16 NC_000016.9:g.1570333C>A
GRCh37.p13 chr 16 NC_000016.9:g.1570333C>T
IFT140 RefSeqGene NG_032783.1:g.96777G>T
IFT140 RefSeqGene NG_032783.1:g.96777G>A
Gene: IFT140, intraflagellar transport 140 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IFT140 transcript NM_014714.4:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog NP_055529.2:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript NM_014714.4:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog NP_055529.2:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X13 XM_005255725.6:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X20 XM_005255726.5:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X11 XM_011522769.4:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X15 XM_011522771.4:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X18 XM_011522772.4:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X12 XM_047434972.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X14 XM_047434973.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X16 XM_047434974.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X17 XM_047434975.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X19 XM_047434976.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X21 XM_047434977.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X22 XM_047434978.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X23 XM_047434979.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X24 XM_047434980.1:c. N/A Genic Downstream Transcript Variant
IFT140 transcript variant X9 XM_011522767.2:c.2697G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X3 XP_011521069.1:p.Ala899= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X9 XM_011522767.2:c.2697G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X3 XP_011521069.1:p.Ala899= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X1 XM_006720991.4:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_006721054.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X1 XM_006720991.4:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_006721054.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X2 XM_047434965.1:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290921.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X2 XM_047434965.1:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290921.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X3 XM_047434966.1:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290922.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X3 XM_047434966.1:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290922.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X4 XM_006720990.4:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_006721053.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X4 XM_006720990.4:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_006721053.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X5 XM_047434967.1:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290923.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X5 XM_047434967.1:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290923.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X6 XM_047434968.1:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290924.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X6 XM_047434968.1:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290924.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X7 XM_047434969.1:c.3672G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290925.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X7 XM_047434969.1:c.3672G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X1 XP_047290925.1:p.Ala1224= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X8 XM_047434970.1:c.3426G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X2 XP_047290926.1:p.Ala1142= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X8 XM_047434970.1:c.3426G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X2 XP_047290926.1:p.Ala1142= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X10 XM_047434971.1:c.1857G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X4 XP_047290927.1:p.Ala619= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X10 XM_047434971.1:c.1857G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X4 XP_047290927.1:p.Ala619= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X25 XM_006720992.4:c.1305G>T A [GCG] > A [GCT] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X11 XP_006721055.1:p.Ala435= A (Ala) > A (Ala) Synonymous Variant
IFT140 transcript variant X25 XM_006720992.4:c.1305G>A A [GCG] > A [GCA] Coding Sequence Variant
intraflagellar transport protein 140 homolog isoform X11 XP_006721055.1:p.Ala435= A (Ala) > A (Ala) Synonymous Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 714754 )
ClinVar Accession Disease Names Clinical Significance
RCV000970689.3 not provided Likely-Benign
RCV001506656.4 Saldino-Mainzer syndrome Likely-Benign
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A T
GRCh38.p14 chr 16 NC_000016.10:g.1520332= NC_000016.10:g.1520332C>A NC_000016.10:g.1520332C>T
GRCh37.p13 chr 16 NC_000016.9:g.1570333= NC_000016.9:g.1570333C>A NC_000016.9:g.1570333C>T
IFT140 RefSeqGene NG_032783.1:g.96777= NG_032783.1:g.96777G>T NG_032783.1:g.96777G>A
IFT140 transcript NM_014714.4:c.3672= NM_014714.4:c.3672G>T NM_014714.4:c.3672G>A
IFT140 transcript NM_014714.3:c.3672= NM_014714.3:c.3672G>T NM_014714.3:c.3672G>A
IFT140 transcript variant X1 XM_006720991.4:c.3672= XM_006720991.4:c.3672G>T XM_006720991.4:c.3672G>A
IFT140 transcript variant X1 XM_006720991.3:c.3672= XM_006720991.3:c.3672G>T XM_006720991.3:c.3672G>A
IFT140 transcript variant X2 XM_006720991.2:c.3672= XM_006720991.2:c.3672G>T XM_006720991.2:c.3672G>A
IFT140 transcript variant X6 XM_006720991.1:c.3672= XM_006720991.1:c.3672G>T XM_006720991.1:c.3672G>A
IFT140 transcript variant X25 XM_006720992.4:c.1305= XM_006720992.4:c.1305G>T XM_006720992.4:c.1305G>A
IFT140 transcript variant X12 XM_006720992.3:c.1305= XM_006720992.3:c.1305G>T XM_006720992.3:c.1305G>A
IFT140 transcript variant X12 XM_006720992.2:c.1305= XM_006720992.2:c.1305G>T XM_006720992.2:c.1305G>A
IFT140 transcript variant X7 XM_006720992.1:c.1305= XM_006720992.1:c.1305G>T XM_006720992.1:c.1305G>A
IFT140 transcript variant X4 XM_006720990.4:c.3672= XM_006720990.4:c.3672G>T XM_006720990.4:c.3672G>A
IFT140 transcript variant X2 XM_006720990.3:c.3672= XM_006720990.3:c.3672G>T XM_006720990.3:c.3672G>A
IFT140 transcript variant X1 XM_006720990.2:c.3672= XM_006720990.2:c.3672G>T XM_006720990.2:c.3672G>A
IFT140 transcript variant X5 XM_006720990.1:c.3672= XM_006720990.1:c.3672G>T XM_006720990.1:c.3672G>A
IFT140 transcript variant X9 XM_011522767.2:c.2697= XM_011522767.2:c.2697G>T XM_011522767.2:c.2697G>A
IFT140 transcript variant X5 XM_011522767.1:c.2697= XM_011522767.1:c.2697G>T XM_011522767.1:c.2697G>A
IFT140 transcript variant X6 XM_047434968.1:c.3672= XM_047434968.1:c.3672G>T XM_047434968.1:c.3672G>A
IFT140 transcript variant X5 XM_047434967.1:c.3672= XM_047434967.1:c.3672G>T XM_047434967.1:c.3672G>A
IFT140 transcript variant X3 XM_047434966.1:c.3672= XM_047434966.1:c.3672G>T XM_047434966.1:c.3672G>A
IFT140 transcript variant X7 XM_047434969.1:c.3672= XM_047434969.1:c.3672G>T XM_047434969.1:c.3672G>A
IFT140 transcript variant X8 XM_047434970.1:c.3426= XM_047434970.1:c.3426G>T XM_047434970.1:c.3426G>A
IFT140 transcript variant X2 XM_047434965.1:c.3672= XM_047434965.1:c.3672G>T XM_047434965.1:c.3672G>A
IFT140 transcript variant X10 XM_047434971.1:c.1857= XM_047434971.1:c.1857G>T XM_047434971.1:c.1857G>A
intraflagellar transport protein 140 homolog NP_055529.2:p.Ala1224= NP_055529.2:p.Ala1224= NP_055529.2:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X1 XP_006721054.1:p.Ala1224= XP_006721054.1:p.Ala1224= XP_006721054.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X11 XP_006721055.1:p.Ala435= XP_006721055.1:p.Ala435= XP_006721055.1:p.Ala435=
intraflagellar transport protein 140 homolog isoform X1 XP_006721053.1:p.Ala1224= XP_006721053.1:p.Ala1224= XP_006721053.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X3 XP_011521069.1:p.Ala899= XP_011521069.1:p.Ala899= XP_011521069.1:p.Ala899=
intraflagellar transport protein 140 homolog isoform X1 XP_047290924.1:p.Ala1224= XP_047290924.1:p.Ala1224= XP_047290924.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X1 XP_047290923.1:p.Ala1224= XP_047290923.1:p.Ala1224= XP_047290923.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X1 XP_047290922.1:p.Ala1224= XP_047290922.1:p.Ala1224= XP_047290922.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X1 XP_047290925.1:p.Ala1224= XP_047290925.1:p.Ala1224= XP_047290925.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X2 XP_047290926.1:p.Ala1142= XP_047290926.1:p.Ala1142= XP_047290926.1:p.Ala1142=
intraflagellar transport protein 140 homolog isoform X1 XP_047290921.1:p.Ala1224= XP_047290921.1:p.Ala1224= XP_047290921.1:p.Ala1224=
intraflagellar transport protein 140 homolog isoform X4 XP_047290927.1:p.Ala619= XP_047290927.1:p.Ala619= XP_047290927.1:p.Ala619=
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

6 SubSNP, 7 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1692069263 Apr 01, 2015 (144)
2 EVA_EXAC ss1692069264 Apr 01, 2015 (144)
3 GNOMAD ss2741621501 Nov 08, 2017 (151)
4 GNOMAD ss4295425877 Apr 26, 2021 (155)
5 TOPMED ss5004726055 Apr 26, 2021 (155)
6 EVA ss5845980140 Oct 16, 2022 (156)
7 ExAC

Submission ignored due to conflicting rows:
Row 2460557 (NC_000016.9:1570332:C:C 121103/121104, NC_000016.9:1570332:C:A 1/121104)
Row 2460558 (NC_000016.9:1570332:C:C 121098/121104, NC_000016.9:1570332:C:T 6/121104)

- Oct 12, 2018 (152)
8 ExAC

Submission ignored due to conflicting rows:
Row 2460557 (NC_000016.9:1570332:C:C 121103/121104, NC_000016.9:1570332:C:A 1/121104)
Row 2460558 (NC_000016.9:1570332:C:C 121098/121104, NC_000016.9:1570332:C:T 6/121104)

- Oct 12, 2018 (152)
9 gnomAD - Genomes NC_000016.10 - 1520332 Apr 26, 2021 (155)
10 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 10893705 (NC_000016.9:1570332:C:C 251035/251038, NC_000016.9:1570332:C:A 3/251038)
Row 10893706 (NC_000016.9:1570332:C:C 251026/251038, NC_000016.9:1570332:C:T 12/251038)

- Jul 13, 2019 (153)
11 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 10893705 (NC_000016.9:1570332:C:C 251035/251038, NC_000016.9:1570332:C:A 3/251038)
Row 10893706 (NC_000016.9:1570332:C:C 251026/251038, NC_000016.9:1570332:C:T 12/251038)

- Jul 13, 2019 (153)
12 TopMed NC_000016.10 - 1520332 Apr 26, 2021 (155)
13 ALFA NC_000016.10 - 1520332 Apr 26, 2021 (155)
14 ClinVar RCV000970689.3 Oct 16, 2022 (156)
15 ClinVar RCV001506656.4 Oct 16, 2022 (156)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1692069264, ss2741621501 NC_000016.9:1570332:C:A NC_000016.10:1520331:C:A (self)
9489699038 NC_000016.10:1520331:C:A NC_000016.10:1520331:C:A (self)
ss1692069263, ss2741621501, ss5845980140 NC_000016.9:1570332:C:T NC_000016.10:1520331:C:T (self)
RCV000970689.3, RCV001506656.4, 480253130, 220271716, 9489699038, ss4295425877, ss5004726055 NC_000016.10:1520331:C:T NC_000016.10:1520331:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs765766910

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07