Variant report

Variant	rs3904056
Chromosome Location	chr6:132044196-132044197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10457575	0.96[ASN][1000 genomes]
rs12192518	0.84[CHB][hapmap]
rs12199015	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12199875	0.83[ASN][1000 genomes]
rs12204520	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12206403	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12206779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12210900	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12530416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17060552	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2270089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286453	0.81[ASW][hapmap];0.90[CHB][hapmap]
rs2286454	0.83[CEU][hapmap]
rs28671630	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3213694	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs365475	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3778569	0.81[ASN][1000 genomes]
rs3778570	0.82[ASN][1000 genomes]
rs3778571	0.83[ASN][1000 genomes]
rs3800193	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs3800194	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs3800195	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs3800198	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800199	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800200	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3843996	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3850247	0.81[ASN][1000 genomes]
rs3850249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3861467	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3861468	0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4126646	0.81[ASN][1000 genomes]
rs4897536	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55931014	0.81[ASN][1000 genomes]
rs60507180	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569753	0.85[CHB][hapmap]
rs6901900	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs6908953	0.96[ASN][1000 genomes]
rs6909448	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs6922526	0.82[ASN][1000 genomes]
rs6922673	0.81[ASN][1000 genomes]
rs6931997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6941622	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73001214	0.81[ASN][1000 genomes]
rs73554727	0.96[ASN][1000 genomes]
rs7738667	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745372	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7746945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7762879	0.84[CHB][hapmap]
rs7765347	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321308	0.90[CHB][hapmap]
rs9483311	0.84[CHB][hapmap]
rs9483321	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs9483334	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9483335	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs9493038	0.84[CHB][hapmap]
rs9493048	0.84[CHB][hapmap]
rs9493050	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs9493057	0.84[ASN][1000 genomes]
rs9493081	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9493082	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9493083	0.95[ASN][1000 genomes]
rs9493084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv830809	chr6:131953928-132126417	Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830810	chr6:131960923-132138396	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv886669	chr6:131991532-132059074	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1810897	chr6:132018366-132045096	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3904056	EPB41L2	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131998600-132054000	Weak transcription	Fetal Intestine Small	intestine
2	chr6:132002600-132054400	Weak transcription	K562	blood
3	chr6:132040200-132047400	Strong transcription	HepG2	liver
4	chr6:132040600-132063200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:132041400-132048600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:132043000-132049800	Weak transcription	Fetal Kidney	kidney
7	chr6:132043400-132044200	Enhancers	Gastric	stomach
8	chr6:132043400-132047200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:132043600-132044200	Enhancers	Stomach Mucosa	stomach
10	chr6:132043600-132044800	Strong transcription	Fetal Intestine Large	intestine
11	chr6:132043800-132047200	Weak transcription	Liver	Liver
12	chr6:132044000-132047600	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links