Variant report

Variant	rs1504135
Chromosome Location	chr2:128003251-128003252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1011019	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10496661	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679414	1.00[ASN][1000 genomes]
rs11680877	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680949	0.87[AMR][1000 genomes]
rs11683986	1.00[ASN][1000 genomes]
rs11691916	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11692990	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105051	0.87[EUR][1000 genomes]
rs13030463	1.00[ASN][1000 genomes]
rs1518760	1.00[ASN][1000 genomes]
rs1568278	1.00[ASN][1000 genomes]
rs2069895	1.00[ASN][1000 genomes]
rs2069898	1.00[ASN][1000 genomes]
rs2069902	1.00[ASN][1000 genomes]
rs2069904	1.00[ASN][1000 genomes]
rs2069919	1.00[ASN][1000 genomes]
rs2404534	0.81[EUR][1000 genomes]
rs2896979	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3958415	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150400	1.00[ASN][1000 genomes]
rs4150402	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150404	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150416	1.00[ASN][1000 genomes]
rs4150421	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150471	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150474	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150476	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4150499	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150523	1.00[ASN][1000 genomes]
rs4662713	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662716	0.81[EUR][1000 genomes]
rs4662718	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662719	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662720	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55998444	1.00[ASN][1000 genomes]
rs56273408	1.00[ASN][1000 genomes]
rs5937	1.00[ASN][1000 genomes]
rs59378658	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61422716	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157508	0.89[EUR][1000 genomes]
rs6430933	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430936	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430938	1.00[ASN][1000 genomes]
rs6731332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6733478	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738690	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6757492	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72845944	1.00[ASN][1000 genomes]
rs72845975	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845976	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845991	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845993	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845997	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72846002	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848604	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72848612	1.00[ASN][1000 genomes]
rs72848615	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72848616	1.00[ASN][1000 genomes]
rs72848618	1.00[ASN][1000 genomes]
rs7556675	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556756	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7562428	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7607907	1.00[ASN][1000 genomes]
rs873270	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1504135	ERCC3	cis	Nerve Tibial	GTEx
rs1504135	ERCC3	cis	Thyroid	GTEx
rs1504135	ERCC3	cis	Adipose Subcutaneous	GTEx
rs1504135	ERCC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127984600-128012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:127989400-128013000	Weak transcription	Pancreas	Pancrea
3	chr2:127996400-128013400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:127996400-128013400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:127999200-128012200	Weak transcription	Liver	Liver
6	chr2:128000000-128013400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:128000400-128013400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:128001400-128012000	Weak transcription	A549	lung
9	chr2:128002400-128015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:128002800-128014000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:128003000-128016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links