SNP Links for PMC (Select 2628742) - SNP

Select item 112653521.

rs11265352 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G,T [Show Flanks]
Chromosome:: 1:160189300 (GRCh38)
1:160159090 (GRCh37)
Canonical SPDI:: NC_000001.11:160189299:A:G,NC_000001.11:160189299:A:T
Gene:: CASQ1 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.385982/75559 (ALFA)
A=0.21564/91 (SGDP_PRJ)
A=0.218679/3665 (TOMMO)
A=0.232143/13 (Siberian)
A=0.278498/816 (KOREAN)
A=0.28821/528 (Korea1K)
A=0.35/14 (GENOME_DK)
A=0.373333/224 (NorthernSweden)
A=0.376492/1451 (ALSPAC)
A=0.386462/1433 (TWINSUK)
A=0.388088/808 (HGDP_Stanford)
A=0.393939/26 (PRJEB36033)
A=0.398214/1784 (Estonian)
A=0.416834/416 (GoNL)
G=0.465645/881 (HapMap)
A=0.478295/2395 (1000Genomes)
G=0.486111/105 (Qatari)
A=0.489647/68437 (GnomAD)
A=0.490804/129911 (TOPMED)
HGVS:: NC_000001.11:g.160189300A>G, NC_000001.11:g.160189300A>T, NC_000001.10:g.160159090A>G, NC_000001.10:g.160159090A>T, NG_042040.1:g.3806A>G, NG_042040.1:g.3806A>T

PubMed

Select item 112651982.

rs11265198 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C,T [Show Flanks]
Chromosome:: 1:159450517 (GRCh38)
1:159420307 (GRCh37)
Canonical SPDI:: NC_000001.11:159450516:G:A,NC_000001.11:159450516:G:C,NC_000001.11:159450516:G:T
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.195541/5490 (ALFA)
C=0./0 (KOREAN)
G=0./0 (Korea1K)
G=0.000071/1 (TOMMO)
G=0.01183/53 (Estonian)
G=0.017857/1 (Siberian)
G=0.02/12 (NorthernSweden)
G=0.022044/22 (GoNL)
G=0.022574/87 (ALSPAC)
G=0.025/1 (GENOME_DK)
G=0.027238/101 (TWINSUK)
G=0.048872/26 (SGDP_PRJ)
G=0.211238/29447 (GnomAD)
G=0.222343/58852 (TOPMED)
G=0.228139/1143 (1000Genomes)
G=0.328704/71 (Qatari)
G=0.381818/588 (HapMap)
HGVS:: NC_000001.11:g.159450517G>A, NC_000001.11:g.159450517G>C, NC_000001.11:g.159450517G>T, NC_000001.10:g.159420307G>A, NC_000001.10:g.159420307G>C, NC_000001.10:g.159420307G>T, NW_025791759.1:g.202344G>A, NW_025791759.1:g.202344G>C, NW_025791759.1:g.202344G>T

PubMed

Select item 75286843.

rs7528684 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G,T [Show Flanks]
Chromosome:: 1:157701026 (GRCh38)
1:157670816 (GRCh37)
Canonical SPDI:: NC_000001.11:157701025:A:C,NC_000001.11:157701025:A:G,NC_000001.11:157701025:A:T
Gene:: FCRL3 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.45994/129475 (ALFA)
T=0./0 (KOREAN)
A=0.29064/118 (SGDP_PRJ)
A=0.321596/548 (HapMap)
A=0.357255/28111 (PAGE_STUDY)
G=0.365402/1637 (Estonian)
G=0.375399/235 (Chileans)
G=0.382609/6413 (TOMMO)
G=0.399563/732 (Korea1K)
G=0.402532/318 (PRJEB37584)
G=0.411215/88 (Vietnamese)
A=0.420084/111192 (TOPMED)
A=0.425/17 (Siberian)
A=0.428995/60043 (GnomAD)
A=0.442067/2214 (1000Genomes)
A=0.444444/24 (PRJEB36033)
G=0.447327/1724 (ALSPAC)
G=0.45/18 (GENOME_DK)
G=0.453333/272 (NorthernSweden)
A=0.453704/98 (Qatari)
G=0.467098/1732 (TWINSUK)
G=0.46994/469 (GoNL)
HGVS:: NC_000001.11:g.157701026A>C, NC_000001.11:g.157701026A>G, NC_000001.11:g.157701026A>T, NC_000001.10:g.157670816A>C, NC_000001.10:g.157670816A>G, NC_000001.10:g.157670816A>T, NG_023241.1:g.4832T>G, NG_023241.1:g.4832T>C, NG_023241.1:g.4832T>A

PubMed LitVar

Select item 28147784.

rs2814778 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 1:159204893 (GRCh38)
1:159174683 (GRCh37)
Canonical SPDI:: NC_000001.11:159204892:T:C
Gene:: ACKR1 (Varview)
Functional Consequence:: 5_prime_UTR_variant
Clinical significance:: protective,pathogenic,association
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.05187/10894 (ALFA)
C=0./0 (PRJEB36033)
C=0.000035/1 (TOMMO)
C=0.000446/2 (Estonian)
C=0.002004/2 (GoNL)
C=0.002157/8 (TWINSUK)
C=0.002595/10 (ALSPAC)
C=0.018727/10 (MGP)
T=0.0625/5 (SGDP_PRJ)
C=0.249452/1139 (GoESP)
C=0.257187/36020 (GnomAD)
C=0.281543/1410 (1000Genomes)
T=0.370238/311 (HapMap)
C=0.430556/93 (Qatari)
HGVS:: NC_000001.11:g.159204893T>C, NC_000001.10:g.159174683T>C, NG_011626.3:g.5881T>C, NM_002036.4:c.-67T>C, NM_002036.3:c.-67T>C, NM_001122951.3:c.-111T>C, NG_051933.1:g.38330T>C

PubMed LitVar

Select item 28144785.

rs2814478 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G,T [Show Flanks]
Chromosome:: 6:47973528 (GRCh38)
6:47941264 (GRCh37)
Canonical SPDI:: NC_000006.12:47973527:A:C,NC_000006.12:47973527:A:G,NC_000006.12:47973527:A:T
Gene:: PTCHD4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.029939/571 (ALFA)
C=0./0 (KOREAN)
A=0./0 (Korea1K)
A=0./0 (TOMMO)
A=0./0 (Vietnamese)
A=0.006061/2 (HapMap)
A=0.016129/9 (SGDP_PRJ)
A=0.017857/1 (Siberian)
A=0.01942/87 (Estonian)
A=0.021237/106 (1000Genomes)
A=0.025807/2031 (PAGE_STUDY)
A=0.027778/6 (Qatari)
A=0.029058/29 (GoNL)
A=0.030358/117 (ALSPAC)
A=0.030812/4322 (GnomAD)
A=0.030878/8173 (TOPMED)
A=0.033333/20 (NorthernSweden)
A=0.03425/127 (TWINSUK)
A=0.05/2 (GENOME_DK)
HGVS:: NC_000006.12:g.47973528A>C, NC_000006.12:g.47973528A>G, NC_000006.12:g.47973528A>T, NC_000006.11:g.47941264A>C, NC_000006.11:g.47941264A>G, NC_000006.11:g.47941264A>T

PubMed

Select item 27687446.

rs2768744 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 1:156902357 (GRCh38)
1:156872149 (GRCh37)
Canonical SPDI:: NC_000001.11:156902356:G:A
Gene:: PEAR1 (Varview)
Functional Consequence:: intron_variant,genic_upstream_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.249057/36598 (ALFA)
A=0.003745/2 (MGP)
A=0.16754/2808 (TOMMO)
G=0.188333/113 (NorthernSweden)
G=0.190381/190 (GoNL)
G=0.194714/722 (TWINSUK)
G=0.195641/754 (ALSPAC)
G=0.201116/901 (Estonian)
A=0.201923/42 (Vietnamese)
A=0.205119/601 (KOREAN)
A=0.21179/388 (Korea1K)
G=0.22/11 (Siberian)
A=0.229592/180 (PRJEB37584)
G=0.25/10 (GENOME_DK)
G=0.320513/100 (SGDP_PRJ)
G=0.347222/75 (Qatari)
A=0.371622/110 (HapMap)
A=0.379314/29849 (PAGE_STUDY)
A=0.396315/1985 (1000Genomes)
G=0.414761/58069 (GnomAD)
G=0.442839/117215 (TOPMED)
HGVS:: NC_000001.11:g.156902357G>A, NC_000001.10:g.156872149G>A

PubMed LitVar

Select item 24944937.

rs2494493 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 1:159840450 (GRCh38)
1:159810240 (GRCh37)
Canonical SPDI:: NC_000001.11:159840449:A:C
Gene:: SNHG28 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.145696/10403 (ALFA)
C=0.068527/307 (Estonian)
C=0.075/3 (GENOME_DK)
C=0.099637/384 (ALSPAC)
C=0.102481/380 (TWINSUK)
C=0.105/63 (NorthernSweden)
C=0.113226/113 (GoNL)
C=0.163265/16 (PRJEB36033)
C=0.258132/36059 (GnomAD)
C=0.274714/72714 (TOPMED)
C=0.310185/67 (Qatari)
C=0.31094/648 (HGDP_Stanford)
A=0.354167/102 (SGDP_PRJ)
C=0.369457/1850 (1000Genomes)
A=0.385122/6455 (TOMMO)
C=0.437104/827 (HapMap)
A=0.47107/863 (Korea1K)
A=0.493857/1447 (KOREAN)
A=0.5/106 (Vietnamese)
A=0.5/9 (Siberian)
HGVS:: NC_000001.11:g.159840450A>C, NC_000001.10:g.159810240A>C

PubMed

Select item 23098798.

rs2309879 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G,T [Show Flanks]
Chromosome:: 1:157440899 (GRCh38)
1:157410689 (GRCh37)
Canonical SPDI:: NC_000001.11:157440898:C:A,NC_000001.11:157440898:C:G,NC_000001.11:157440898:C:T
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
G=0.041667/9 (Vietnamese)
G=0.08024/147 (Korea1K)
G=0.081229/238 (KOREAN)
G=0.106703/1788 (TOMMO)
G=0.19441/974 (1000Genomes)
G=0.271667/163 (NorthernSweden)
G=0.289712/76684 (TOPMED)
G=0.301786/1352 (Estonian)
G=0.319444/69 (Qatari)
C=0.333333/6 (Siberian)
G=0.337052/1299 (ALSPAC)
G=0.342685/342 (GoNL)
G=0.345739/1282 (TWINSUK)
C=0.433333/65 (SGDP_PRJ)
G=0.45/18 (GENOME_DK)
G=0.456522/147 (HapMap)
HGVS:: NC_000001.11:g.157440899C>A, NC_000001.11:g.157440899C>G, NC_000001.11:g.157440899C>T, NC_000001.10:g.157410689C>A, NC_000001.10:g.157410689C>G, NC_000001.10:g.157410689C>T

PubMed

Select item 8578599.

rs857859 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A,C,G [Show Flanks]
Chromosome:: 1:158801660 (GRCh38)
1:158771450 (GRCh37)
Canonical SPDI:: NC_000001.11:158801659:T:A,NC_000001.11:158801659:T:C,NC_000001.11:158801659:T:G
Gene:: OR6N1 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.438894/7872 (ALFA)
G=0./0 (KOREAN)
T=0.20892/89 (SGDP_PRJ)
A=0.325/13 (GENOME_DK)
A=0.331667/199 (NorthernSweden)
T=0.346154/9 (Siberian)
T=0.347997/5832 (TOMMO)
A=0.350545/1351 (ALSPAC)
A=0.35356/1311 (TWINSUK)
A=0.356713/356 (GoNL)
T=0.366958/1838 (1000Genomes)
T=0.368098/120 (HapMap)
A=0.369196/1654 (Estonian)
T=0.397196/85 (Vietnamese)
T=0.416485/763 (Korea1K)
T=0.459485/121621 (TOPMED)
T=0.474322/66407 (GnomAD)
T=0.490741/106 (Qatari)
HGVS:: NC_000001.11:g.158801660T>A, NC_000001.11:g.158801660T>C, NC_000001.11:g.158801660T>G, NC_000001.10:g.158771450T>A, NC_000001.10:g.158771450T>C, NC_000001.10:g.158771450T>G

PubMed

Select item 69107710.

rs691077 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 1:158222163 (GRCh38)
1:158191953 (GRCh37)
Canonical SPDI:: NC_000001.11:158222162:T:C
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.301256/5566 (ALFA)
T=0.1/4 (GENOME_DK)
T=0.207071/123 (NorthernSweden)
T=0.219892/975 (Estonian)
T=0.265625/119 (SGDP_PRJ)
T=0.295455/13 (Siberian)
T=0.374297/51784 (GnomAD)
T=0.37963/82 (Qatari)
T=0.392263/103828 (TOPMED)
T=0.414071/6940 (TOMMO)
T=0.42901/1257 (KOREAN)
T=0.43286/793 (Korea1K)
T=0.471429/132 (HapMap)
T=0.484385/2426 (1000Genomes)
HGVS:: NC_000001.11:g.158222163T>C, NC_000001.10:g.158191953T>C

PubMed

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