SNP Links for Gene (Select 4498) - SNP

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Select item 14910806881.

rs1491080688 has merged into rs35988004 [Homo sapiens]

Variant type:: DELINS
Alleles:: TT>-,T,TTT,TTTT [Show Flanks]
Chromosome:: 16:56637005 (GRCh38)
16:56670917 (GRCh37)
Canonical SPDI:: NC_000016.10:56636996:TTTTTTTTTT:TTTTTTTT,NC_000016.10:56636996:TTTTTTTTTT:TTTTTTTTT,NC_000016.10:56636996:TTTTTTTTTT:TTTTTTTTTTT,NC_000016.10:56636996:TTTTTTTTTT:TTTTTTTTTTTT
Gene:: MT1A (Varview), MT1JP (Varview)
Functional Consequence:: non_coding_transcript_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTT=0./0 (ALFA)
-=0.225/9 (GENOME_DK)
-=0.255/153 (NorthernSweden)
-=0.256104/4292 (TOMMO)
-=0.281114/515 (Korea1K)
-=0.285677/1101 (ALSPAC)
-=0.298813/1108 (TWINSUK)
-=0.33642/89047 (TOPMED)
-=0.362618/1812 (1000Genomes)
HGVS:: NC_000016.10:g.56637005_56637006del, NC_000016.10:g.56637006del, NC_000016.10:g.56637006dup, NC_000016.10:g.56637005_56637006dup, NC_000016.9:g.56670917_56670918del, NC_000016.9:g.56670918del, NC_000016.9:g.56670918dup, NC_000016.9:g.56670917_56670918dup, NM_175622.3:c.*125_*126del, NM_175622.3:c.*126del, NM_175622.3:c.*126dup, NM_175622.3:c.*125_*126dup, NM_175622.2:c.*62_*63del, NM_175622.2:c.*63del, NM_175622.2:c.*63dup, NM_175622.2:c.*62_*63dup, NR_036677.1:n.327_328del, NR_036677.1:n.328del, NR_036677.1:n.328dup, NR_036677.1:n.327_328dup

Select item 14908394052.

rs1490839405 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 16:56636489 (GRCh38)
16:56670401 (GRCh37)
Canonical SPDI:: NC_000016.10:56636488:A:C
Gene:: MT1JP (Varview)
Functional Consequence:: non_coding_transcript_variant
Validated:: by frequency
MAF:: C=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000016.10:g.56636489A>C, NC_000016.9:g.56670401A>C, NM_175622.3:c.79A>C, NM_175622.2:c.79A>C, NR_036677.1:n.158A>C, NM_175622.1:c.79A>C

Select item 14907853753.

rs1490785375 [Homo sapiens]

Variant type:: DELINS
Alleles:: ATTTT>- [Show Flanks]
Chromosome:: 16:56634618 (GRCh38)
16:56668530 (GRCh37)
Canonical SPDI:: NC_000016.10:56634612:ATTTTATTTT:ATTTT
Gene:: MT1JP (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: ATTTTATTTT=0./0 (ALFA)
-=0.000008/2 (TOPMED)
HGVS:: NC_000016.10:g.56634613ATTTT[1], NC_000016.9:g.56668525ATTTT[1], NG_030326.1:g.6992ATTTT[1]

Select item 14906501664.

rs1490650166 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:56635029 (GRCh38)
16:56668941 (GRCh37)
Canonical SPDI:: NC_000016.10:56635028:C:T
Gene:: MT1JP (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
HGVS:: NC_000016.10:g.56635029C>T, NC_000016.9:g.56668941C>T, NG_030326.1:g.7408C>T

Select item 14906258285.

rs1490625828 [Homo sapiens]

Variant type:: DELINS
Alleles:: C>- [Show Flanks]
Chromosome:: 16:56634175 (GRCh38)
16:56668087 (GRCh37)
Canonical SPDI:: NC_000016.10:56634174:CC:C
Gene:: MT1JP (Varview), MT1M (Varview)
Functional Consequence:: 2KB_upstream_variant,500B_downstream_variant,downstream_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CC=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.56634176del, NC_000016.9:g.56668088del, NG_030326.1:g.6555del

Select item 14901383056.

rs1490138305 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:56634107 (GRCh38)
16:56668019 (GRCh37)
Canonical SPDI:: NC_000016.10:56634106:C:T
Gene:: MT1JP (Varview), MT1M (Varview)
Functional Consequence:: 2KB_upstream_variant,500B_downstream_variant,downstream_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000023/6 (TOPMED)
HGVS:: NC_000016.10:g.56634107C>T, NC_000016.9:g.56668019C>T, NG_030326.1:g.6486C>T

Select item 14886100397.

rs1488610039 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:56635990 (GRCh38)
16:56669902 (GRCh37)
Canonical SPDI:: NC_000016.10:56635989:C:T
Gene:: MT1JP (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000016.10:g.56635990C>T, NC_000016.9:g.56669902C>T

Select item 14883711398.

rs1488371139 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:56634930 (GRCh38)
16:56668842 (GRCh37)
Canonical SPDI:: NC_000016.10:56634929:C:T
Gene:: MT1JP (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000008/2 (TOPMED)
HGVS:: NC_000016.10:g.56634930C>T, NC_000016.9:g.56668842C>T, NG_030326.1:g.7309C>T

Select item 14883395339.

rs1488339533 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 16:56636793 (GRCh38)
16:56670705 (GRCh37)
Canonical SPDI:: NC_000016.10:56636792:G:T
Gene:: MT1A (Varview), MT1JP (Varview)
Functional Consequence:: 2KB_upstream_variant,intron_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000011/3 (TOPMED)
HGVS:: NC_000016.10:g.56636793G>T, NC_000016.9:g.56670705G>T

Select item 148825815610.

rs1488258156 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 16:56637292 (GRCh38)
16:56671204 (GRCh37)
Canonical SPDI:: NC_000016.10:56637291:C:T
Gene:: MT1A (Varview), MT1JP (Varview)
Functional Consequence:: 2KB_upstream_variant,500B_downstream_variant,downstream_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000016.10:g.56637292C>T, NC_000016.9:g.56671204C>T

Select item 148735516711.

rs1487355167 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 16:56637186 (GRCh38)
16:56671098 (GRCh37)
Canonical SPDI:: NC_000016.10:56637185:T:C
Gene:: MT1A (Varview), MT1JP (Varview)
Functional Consequence:: upstream_transcript_variant,500B_downstream_variant,downstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000011/3 (TOPMED)
C=0.000071/2 (TOMMO)
HGVS:: NC_000016.10:g.56637186T>C, NC_000016.9:g.56671098T>C

Select item 148730997712.

rs1487309977 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:56635097 (GRCh38)
16:56669009 (GRCh37)
Canonical SPDI:: NC_000016.10:56635096:G:A
Gene:: MT1JP (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000014/2 (GnomAD)
A=0.000015/4 (TOPMED)
HGVS:: NC_000016.10:g.56635097G>A, NC_000016.9:g.56669009G>A, NG_030326.1:g.7476G>A

Select item 148667918813.

rs1486679188 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: 16:56634829 (GRCh38)
16:56668741 (GRCh37)
Canonical SPDI:: NC_000016.10:56634828:G:A,NC_000016.10:56634828:G:T
Gene:: MT1JP (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.56634829G>A, NC_000016.10:g.56634829G>T, NC_000016.9:g.56668741G>A, NC_000016.9:g.56668741G>T, NG_030326.1:g.7208G>A, NG_030326.1:g.7208G>T

Select item 148642751814.

rs1486427518 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 16:56633782 (GRCh38)
16:56667694 (GRCh37)
Canonical SPDI:: NC_000016.10:56633781:C:G
Gene:: MT1JP (Varview), MT1M (Varview)
Functional Consequence:: coding_sequence_variant,upstream_transcript_variant,synonymous_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000014/2 (GnomAD)
HGVS:: NC_000016.10:g.56633782C>G, NC_000016.9:g.56667694C>G, NG_030326.1:g.6161C>G, NM_176870.3:c.126C>G, NM_176870.2:c.126C>G

Select item 148613088115.

rs1486130881 [Homo sapiens]

Variant type:: DELINS
Alleles:: CTT>- [Show Flanks]
Chromosome:: 16:56637098 (GRCh38)
16:56671010 (GRCh37)
Canonical SPDI:: NC_000016.10:56637092:TTCTTCTT:TTCTT
Gene:: MT1A (Varview), MT1JP (Varview)
Functional Consequence:: upstream_transcript_variant,500B_downstream_variant,downstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTCTT=0.000071/1 (ALFA)
-=0.000038/10 (TOPMED)
-=0.000043/6 (GnomAD)
HGVS:: NC_000016.10:g.56637095CTT[1], NC_000016.9:g.56671007CTT[1]

Select item 148552668016.

rs1485526680 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 16:56636694 (GRCh38)
16:56670606 (GRCh37)
Canonical SPDI:: NC_000016.10:56636693:A:G
Gene:: MT1A (Varview), MT1JP (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
HGVS:: NC_000016.10:g.56636694A>G, NC_000016.9:g.56670606A>G

Select item 148431583517.

rs1484315835 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 16:56634262 (GRCh38)
16:56668174 (GRCh37)
Canonical SPDI:: NC_000016.10:56634261:G:A
Gene:: MT1JP (Varview), MT1M (Varview)
Functional Consequence:: upstream_transcript_variant,500B_downstream_variant,downstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.56634262G>A, NC_000016.9:g.56668174G>A, NG_030326.1:g.6641G>A

Select item 148357025118.

rs1483570251 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 16:56634898 (GRCh38)
16:56668810 (GRCh37)
Canonical SPDI:: NC_000016.10:56634897:G:A,NC_000016.10:56634897:G:C
Gene:: MT1JP (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000016.10:g.56634898G>A, NC_000016.10:g.56634898G>C, NC_000016.9:g.56668810G>A, NC_000016.9:g.56668810G>C, NG_030326.1:g.7277G>A, NG_030326.1:g.7277G>C

Select item 148325772319.

rs1483257723 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->A [Show Flanks]
Chromosome:: 16:56633962 (GRCh38)
16:56667875 (GRCh37)
Canonical SPDI:: NC_000016.10:56633962:AAAA:AAAAA
Gene:: MT1JP (Varview), MT1M (Varview)
Functional Consequence:: 3_prime_UTR_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: AAAAA=0./0 (ALFA)
HGVS:: NC_000016.10:g.56633966dup, NC_000016.9:g.56667878dup, NG_030326.1:g.6345dup, NM_176870.3:c.*124dup, NM_176870.2:c.*124dup

Select item 148310859520.

rs1483108595 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->CGTGCGCCGGCTCCTGCA [Show Flanks]
Chromosome:: 16:56636440 (GRCh38)
16:56670353 (GRCh37)
Canonical SPDI:: NC_000016.10:56636440:GGCTCCTGCACGTGCGCCGGCTCCTGCA:GGCTCCTGCACGTGCGCCGGCTCCTGCACGTGCGCCGGCTCCTGCA
Gene:: MT1JP (Varview)
Functional Consequence:: non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGCTCCTGCACGTGCGCCGGCTCCTGCACGTGCGCCGGCTCCTGCA=0./0 (ALFA)
GGCTCCTGCACGTGCGCC=0.000008/2 (TOPMED)
GGCTCCTGCACGTGCGCC=0.000012/3 (GnomAD_exomes)
HGVS:: NC_000016.10:g.56636451_56636468dup, NC_000016.9:g.56670363_56670380dup, NM_175622.3:c.41_58dup, NM_175622.2:c.41_58dup, NR_036677.1:n.120_137dup, NM_175622.1:c.41_58dup

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