Variant report

Variant	rs12476056
Chromosome Location	chr2:114050323-114050324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10864913	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11123176	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123177	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123179	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11685107	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11685421	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11691437	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11695071	0.90[AMR][1000 genomes]
rs12475140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12476331	0.80[AMR][1000 genomes]
rs13015130	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2002510	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36000169	0.92[AMR][1000 genomes]
rs6716573	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7425070	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs935365	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2762785	chr2:114044712-114081784	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12476056	SLC35F5	cis	parietal	SCAN
rs12476056	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs12476056	AC016683.6	cis	lung	GTEx
rs12476056	LOC654433	cis	parietal	SCAN
rs12476056	PAX8	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114049000-114053600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:114049400-114053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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