"human"[ORGN] and MAN2A1 - SNP

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Select item 37976771.

rs3797677 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 5:109842319 (GRCh38)
5:109178020 (GRCh37)
Canonical SPDI:: NC_000005.10:109842318:T:A
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000203/10 (ALFA)
A=0.000223/1 (Estonian)
A=0.000606/85 (GnomAD)
A=0.000729/193 (TOPMED)
A=0.00164/257 (GnomAD_exomes)
A=0.002724/66 (ExAC)
A=0.00463/1 (Vietnamese)
A=0.004841/24 (1000Genomes)
A=0.015625/5 (HapMap)
A=0.040383/118 (KOREAN)
A=0.052402/96 (Korea1K)
A=0.073289/1228 (TOMMO)
T=0.5/1 (Siberian)
T=0.5/6 (SGDP_PRJ)
HGVS:: NC_000005.10:g.109842319T>A, NC_000005.9:g.109178020T>A

Select item 26712.

rs2671 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:109868553 (GRCh38)
5:109204254 (GRCh37)
Canonical SPDI:: NC_000005.10:109868552:C:G
Gene:: MAN2A1 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000007/1 (GnomAD)
HGVS:: NC_000005.10:g.109868553C>G, NC_000005.9:g.109204254C>G, NM_002372.4:c.*1555C>G, NM_002372.3:c.*1555C>G, XM_017009472.2:c.*1555C>G, XM_024446048.2:c.*1555C>G

Select item 35633.

rs3563 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:109868538 (GRCh38)
5:109204239 (GRCh37)
Canonical SPDI:: NC_000005.10:109868537:A:G
Gene:: MAN2A1 (Varview)
Functional Consequence:: 3_prime_UTR_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
G=0.000015/4 (TOPMED)
HGVS:: NC_000005.10:g.109868538A>G, NC_000005.9:g.109204239A>G, NM_002372.4:c.*1540A>G, NM_002372.3:c.*1540A>G, XM_017009472.2:c.*1540A>G, XM_024446048.2:c.*1540A>G

Select item 2487494.

rs248749 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:109694447 (GRCh38)
5:109030148 (GRCh37)
Canonical SPDI:: NC_000005.10:109694446:C:T
Gene:: MAN2A1 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.003812/72 (ALFA)
T=0.001249/6 (1000Genomes)
T=0.00235/622 (TOPMED)
T=0.003092/433 (GnomAD)
T=0.004045/15 (TWINSUK)
T=0.004411/17 (ALSPAC)
T=0.00501/5 (GoNL)
T=0.006667/4 (NorthernSweden)
T=0.008036/36 (Estonian)
T=0.010652/179 (TOMMO)
T=0.010951/32 (KOREAN)
T=0.011463/21 (Korea1K)
C=0.5/1 (Siberian)
C=0.5/5 (SGDP_PRJ)
HGVS:: NC_000005.10:g.109694447C>T, NC_000005.9:g.109030148C>T

Select item 2487505.

rs248750 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:109746528 (GRCh38)
5:109082229 (GRCh37)
Canonical SPDI:: NC_000005.10:109746527:G:A
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0./0 (HapMap)
A=0./0 (TWINSUK)
A=0.000014/2 (GnomAD)
A=0.000015/4 (TOPMED)
A=0.000259/1 (ALSPAC)
HGVS:: NC_000005.10:g.109746528G>A, NC_000005.9:g.109082229G>A

Select item 2487516.

rs248751 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 5:109736099 (GRCh38)
5:109071800 (GRCh37)
Canonical SPDI:: NC_000005.10:109736098:C:A,NC_000005.10:109736098:C:T
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000216/4 (ALFA)
T=0./0 (HapMap)
A=0./0 (KOREAN)
T=0.000236/33 (GnomAD)
T=0.000276/73 (TOPMED)
T=0.000781/5 (1000Genomes)
HGVS:: NC_000005.10:g.109736099C>A, NC_000005.10:g.109736099C>T, NC_000005.9:g.109071800T>C, NC_000005.9:g.109071800T>A

Select item 2487527.

rs248752 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G,T [Show Flanks]
Chromosome:: 5:109731518 (GRCh38)
5:109067219 (GRCh37)
Canonical SPDI:: NC_000005.10:109731517:A:C,NC_000005.10:109731517:A:G,NC_000005.10:109731517:A:T
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0./0 (KOREAN)
A=0./0 (Qatari)
A=0.00187/12 (1000Genomes)
A=0.00204/34 (TOMMO)
A=0.00717/4 (SGDP_PRJ)
A=0.03125/1 (GENOME_DK)
HGVS:: NC_000005.10:g.109731518A>C, NC_000005.10:g.109731518A>G, NC_000005.10:g.109731518A>T, NC_000005.9:g.109067219A>C, NC_000005.9:g.109067219A>G, NC_000005.9:g.109067219A>T

Select item 2487538.

rs248753 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 5:109731715 (GRCh38)
5:109067416 (GRCh37)
Canonical SPDI:: NC_000005.10:109731714:T:G
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.011555/214 (ALFA)
G=0.01/6 (NorthernSweden)
G=0.01493/2091 (GnomAD)
G=0.015303/77 (1000Genomes)
G=0.017024/4506 (TOPMED)
G=0.017857/80 (Estonian)
G=0.02371/397 (TOMMO)
G=0.030116/88 (KOREAN)
G=0.03548/65 (Korea1K)
T=0.428571/12 (SGDP_PRJ)
HGVS:: NC_000005.10:g.109731715T>G, NC_000005.9:g.109067416T>G

Select item 7190889.

rs719088 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 5:109751972 (GRCh38)
5:109087673 (GRCh37)
Canonical SPDI:: NC_000005.10:109751971:T:C
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.076019/1436 (ALFA)
C=0.000071/1 (TOMMO)
C=0.000546/1 (Korea1K)
C=0.000684/2 (KOREAN)
C=0.045455/2 (PRJEB36033)
C=0.060045/269 (Estonian)
C=0.06041/224 (TWINSUK)
C=0.063051/243 (ALSPAC)
C=0.071667/43 (NorthernSweden)
C=0.07515/75 (GoNL)
C=0.078704/17 (Qatari)
C=0.083894/22206 (TOPMED)
C=0.085366/28 (HapMap)
C=0.086362/12095 (GnomAD)
C=0.088226/442 (1000Genomes)
C=0.1/4 (GENOME_DK)
T=0.25/1 (Siberian)
T=0.444444/32 (SGDP_PRJ)
HGVS:: NC_000005.10:g.109751972T>C, NC_000005.9:g.109087673T>C

Select item 72335010.

rs723350 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:109856782 (GRCh38)
5:109192483 (GRCh37)
Canonical SPDI:: NC_000005.10:109856781:C:T
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.366014/6914 (ALFA)
C=0.105065/307 (KOREAN)
C=0.122642/26 (Vietnamese)
C=0.122903/2060 (TOMMO)
C=0.181818/8 (Siberian)
C=0.198795/99 (SGDP_PRJ)
C=0.274691/89 (HapMap)
C=0.295597/1480 (1000Genomes)
C=0.339548/89875 (TOPMED)
C=0.346869/48321 (GnomAD)
C=0.367188/1645 (Estonian)
C=0.375/15 (GENOME_DK)
C=0.383768/383 (GoNL)
C=0.410483/1582 (ALSPAC)
C=0.412037/89 (Qatari)
C=0.42/252 (NorthernSweden)
C=0.421791/1564 (TWINSUK)
HGVS:: NC_000005.10:g.109856782C>T, NC_000005.9:g.109192483C>T

Select item 72421411.

rs724214 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 5:109752655 (GRCh38)
5:109088356 (GRCh37)
Canonical SPDI:: NC_000005.10:109752654:G:C
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.174907/3304 (ALFA)
C=0.150301/150 (GoNL)
C=0.153333/92 (NorthernSweden)
C=0.158037/586 (TWINSUK)
C=0.161908/22683 (GnomAD)
C=0.166149/43978 (TOPMED)
C=0.168396/649 (ALSPAC)
C=0.225/9 (GENOME_DK)
C=0.240741/52 (Qatari)
C=0.241071/1080 (Estonian)
C=0.263636/87 (HapMap)
C=0.265771/1331 (1000Genomes)
G=0.330034/967 (KOREAN)
G=0.345161/107 (SGDP_PRJ)
G=0.369541/677 (Korea1K)
G=0.376354/6308 (TOMMO)
G=0.397196/85 (Vietnamese)
G=0.4375/14 (Siberian)
HGVS:: NC_000005.10:g.109752655G>C, NC_000005.9:g.109088356G>C

Select item 72421512.

rs724215 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 5:109752788 (GRCh38)
5:109088489 (GRCh37)
Canonical SPDI:: NC_000005.10:109752787:A:C
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000029/4 (GnomAD)
C=0.000045/12 (TOPMED)
HGVS:: NC_000005.10:g.109752788A>C, NC_000005.9:g.109088489A>C

Select item 72478313.

rs724783 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 5:109717759 (GRCh38)
5:109053460 (GRCh37)
Canonical SPDI:: NC_000005.10:109717758:T:C
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.356538/6735 (ALFA)
C=0.240741/52 (Qatari)
C=0.242321/710 (KOREAN)
C=0.265284/486 (Korea1K)
C=0.270224/4529 (TOMMO)
C=0.295312/1323 (Estonian)
C=0.311667/187 (NorthernSweden)
C=0.314286/66 (Vietnamese)
C=0.343379/1720 (1000Genomes)
C=0.345615/1332 (ALSPAC)
C=0.346818/1286 (TWINSUK)
C=0.363727/363 (GoNL)
C=0.390738/54690 (GnomAD)
T=0.390756/93 (SGDP_PRJ)
C=0.397454/105202 (TOPMED)
T=0.416667/15 (Siberian)
HGVS:: NC_000005.10:g.109717759T>C, NC_000005.9:g.109053460T>C

Select item 72478414.

rs724784 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 5:109717634 (GRCh38)
5:109053335 (GRCh37)
Canonical SPDI:: NC_000005.10:109717633:A:C
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.418198/14795 (ALFA)
C=0.242662/711 (KOREAN)
C=0.26583/487 (Korea1K)
C=0.270331/4531 (TOMMO)
C=0.310185/67 (Qatari)
C=0.319444/69 (Vietnamese)
C=0.355357/1592 (Estonian)
C=0.375/15 (GENOME_DK)
A=0.375887/106 (SGDP_PRJ)
C=0.383333/230 (NorthernSweden)
A=0.4/16 (Siberian)
C=0.402405/2015 (1000Genomes)
C=0.406688/1508 (TWINSUK)
C=0.408666/1575 (ALSPAC)
C=0.421081/795 (HapMap)
C=0.438878/438 (GoNL)
C=0.450026/62919 (GnomAD)
C=0.453765/120107 (TOPMED)
A=0.486486/36 (PRJEB36033)
HGVS:: NC_000005.10:g.109717634A>C, NC_000005.9:g.109053335A>C

Select item 75980915.

rs759809 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G,T [Show Flanks]
Chromosome:: 5:109830083 (GRCh38)
5:109165784 (GRCh37)
Canonical SPDI:: NC_000005.10:109830082:A:C,NC_000005.10:109830082:A:G,NC_000005.10:109830082:A:T
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
G=0.238908/700 (KOREAN)
G=0.259259/56 (Qatari)
G=0.270197/495 (Korea1K)
G=0.28972/62 (Vietnamese)
G=0.3/12 (GENOME_DK)
G=0.312277/1399 (Estonian)
G=0.314707/5274 (TOMMO)
G=0.318333/191 (NorthernSweden)
G=0.349766/1348 (ALSPAC)
G=0.356257/1321 (TWINSUK)
G=0.36446/1825 (1000Genomes)
G=0.374749/374 (GoNL)
A=0.391473/101 (SGDP_PRJ)
G=0.410494/133 (HapMap)
G=0.414458/109703 (TOPMED)
A=0.444444/16 (Siberian)
HGVS:: NC_000005.10:g.109830083A>C, NC_000005.10:g.109830083A>G, NC_000005.10:g.109830083A>T, NC_000005.9:g.109165784A>C, NC_000005.9:g.109165784A>G, NC_000005.9:g.109165784A>T

Select item 75981016.

rs759810 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A,G [Show Flanks]
Chromosome:: 5:109830486 (GRCh38)
5:109166187 (GRCh37)
Canonical SPDI:: NC_000005.10:109830485:T:A,NC_000005.10:109830485:T:G
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.42137/4405 (ALFA)
T=0.061396/1029 (TOMMO)
T=0.091126/267 (KOREAN)
T=0.092593/20 (Vietnamese)
T=0.23176/108 (SGDP_PRJ)
T=0.24/12 (Siberian)
T=0.37336/1870 (1000Genomes)
T=0.424002/112229 (TOPMED)
T=0.451562/2023 (Estonian)
G=0.473333/284 (NorthernSweden)
T=0.480962/480 (GoNL)
T=0.487545/1879 (ALSPAC)
T=0.490291/1818 (TWINSUK)
G=0.490741/106 (Qatari)
T=0.5/20 (GENOME_DK)
HGVS:: NC_000005.10:g.109830486T>A, NC_000005.10:g.109830486T>G, NC_000005.9:g.109166187T>A, NC_000005.9:g.109166187T>G

Select item 75981117.

rs759811 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G,T [Show Flanks]
Chromosome:: 5:109830822 (GRCh38)
5:109166523 (GRCh37)
Canonical SPDI:: NC_000005.10:109830821:C:A,NC_000005.10:109830821:C:G,NC_000005.10:109830821:C:T
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.347147/6182 (ALFA)
C=0.060125/1008 (TOMMO)
C=0.090785/266 (KOREAN)
C=0.098799/181 (Korea1K)
C=0.099057/21 (Vietnamese)
C=0.173077/9 (Siberian)
C=0.175299/88 (SGDP_PRJ)
C=0.240943/1207 (1000Genomes)
C=0.291704/77211 (TOPMED)
C=0.365179/1636 (Estonian)
C=0.375/15 (GENOME_DK)
C=0.377756/377 (GoNL)
C=0.388889/84 (Qatari)
C=0.39699/1530 (ALSPAC)
C=0.4048/1501 (TWINSUK)
C=0.411667/247 (NorthernSweden)
HGVS:: NC_000005.10:g.109830822C>A, NC_000005.10:g.109830822C>G, NC_000005.10:g.109830822C>T, NC_000005.9:g.109166523C>A, NC_000005.9:g.109166523C>G, NC_000005.9:g.109166523C>T

Select item 75981218.

rs759812 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:109692643 (GRCh38)
5:109028344 (GRCh37)
Canonical SPDI:: NC_000005.10:109692642:A:G
Gene:: MAN2A1 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.159981/3039 (ALFA)
G=0.0046/77 (TOMMO)
G=0.011463/21 (Korea1K)
G=0.011636/34 (KOREAN)
G=0.028037/6 (Vietnamese)
G=0.119769/600 (1000Genomes)
G=0.139631/36959 (TOPMED)
G=0.147168/20622 (GnomAD)
G=0.15/6 (GENOME_DK)
G=0.158846/589 (TWINSUK)
G=0.162325/162 (GoNL)
G=0.162852/185 (Daghestan)
G=0.168656/650 (ALSPAC)
G=0.175/784 (Estonian)
G=0.185/111 (NorthernSweden)
G=0.194444/42 (Qatari)
G=0.2/16 (PRJEB36033)
A=0.416667/5 (Siberian)
A=0.451613/56 (SGDP_PRJ)
HGVS:: NC_000005.10:g.109692643A>G, NC_000005.9:g.109028344A>G

Select item 76366219.

rs763662 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 5:109794568 (GRCh38)
5:109130269 (GRCh37)
Canonical SPDI:: NC_000005.10:109794567:T:A
Gene:: MAN2A1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.065379/1235 (ALFA)
A=0.000071/1 (TOMMO)
A=0.000342/1 (KOREAN)
A=0.000546/1 (Korea1K)
A=0.048214/216 (Estonian)
A=0.050701/188 (TWINSUK)
A=0.050856/196 (ALSPAC)
A=0.056112/56 (GoNL)
A=0.058333/35 (NorthernSweden)
A=0.074074/16 (Qatari)
A=0.075758/25 (HapMap)
A=0.075968/20108 (TOPMED)
A=0.076491/10716 (GnomAD)
A=0.083698/419 (1000Genomes)
A=0.1/4 (GENOME_DK)
T=0.25/1 (Siberian)
T=0.441176/30 (SGDP_PRJ)
HGVS:: NC_000005.10:g.109794568T>A, NC_000005.9:g.109130269T>A

Select item 84573520.

rs845735 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G,T [Show Flanks]
Chromosome:: 5:109688170 (GRCh38)
5:109023871 (GRCh37)
Canonical SPDI:: NC_000005.10:109688169:C:A,NC_000005.10:109688169:C:G,NC_000005.10:109688169:C:T
Gene:: MAN2A1 (Varview), LOC124901041 (Varview)
Functional Consequence:: 3_prime_UTR_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.161726/3055 (ALFA)
T=0./0 (KOREAN)
G=0.136667/82 (NorthernSweden)
G=0.138889/30 (Qatari)
G=0.147295/147 (GoNL)
G=0.15611/21887 (GnomAD)
G=0.165171/43719 (TOPMED)
G=0.197991/887 (Estonian)
G=0.2426/459 (HapMap)
G=0.25/10 (GENOME_DK)
G=0.270924/1357 (1000Genomes)
C=0.331081/98 (SGDP_PRJ)
C=0.373362/684 (Korea1K)
C=0.381379/6392 (TOMMO)
C=0.420561/90 (Vietnamese)
C=0.433333/13 (Siberian)
HGVS:: NC_000005.10:g.109688170C>A, NC_000005.10:g.109688170C>G, NC_000005.10:g.109688170C>T, NC_000005.9:g.109023871C>A, NC_000005.9:g.109023871C>G, NC_000005.9:g.109023871C>T, XM_047417985.1:c.*1220G>T, XM_047417985.1:c.*1220G>C, XM_047417985.1:c.*1220G>A

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