Variant report

Variant	rs655605
Chromosome Location	chr6:161400212-161400213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12173735	0.83[ASN][1000 genomes]
rs13194157	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs1543261	0.91[CEU][hapmap]
rs2872613	0.89[TSI][hapmap];1.00[YRI][hapmap]
rs4472323	0.81[CEU][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs4708898	0.82[CEU][hapmap]
rs4709486	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs4709490	0.91[CEU][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs4709491	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs4709495	0.91[CEU][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs4709496	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs587501	0.92[EUR][1000 genomes]
rs601939	0.88[ASN][1000 genomes]
rs615269	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs619393	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs628430	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs628923	0.86[EUR][1000 genomes]
rs6455701	0.81[CEU][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs647923	0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657551	0.88[EUR][1000 genomes]
rs662541	0.89[EUR][1000 genomes]
rs668638	0.92[EUR][1000 genomes]
rs672043	0.86[ASN][1000 genomes]
rs679240	1.00[ASN][1000 genomes]
rs681455	1.00[ASN][1000 genomes]
rs682110	0.86[EUR][1000 genomes]
rs683549	0.81[EUR][1000 genomes]
rs685388	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900500	0.81[CEU][hapmap]
rs6905942	0.91[CEU][hapmap]
rs6908283	0.86[EUR][1000 genomes]
rs6913706	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6923835	0.81[CEU][hapmap]
rs6925502	0.91[CEU][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6929462	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6933810	0.91[CEU][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs705829	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs705830	0.86[EUR][1000 genomes]
rs7760056	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs9347476	0.90[ASN][1000 genomes]
rs9355324	0.96[ASN][1000 genomes]
rs9355326	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs9355330	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs9355332	0.91[CEU][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs9355858	0.82[ASN][1000 genomes]
rs9355863	0.96[ASN][1000 genomes]
rs9355864	0.96[ASN][1000 genomes]
rs9355873	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs9364586	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs9365248	0.81[CEU][hapmap];1.00[YRI][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	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs655605	LOC729603	cis	cerebellum	SCAN
rs655605	MAP3K4	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161397400-161406800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:161399000-161400400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr6:161399000-161401000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:161399200-161400400	Enhancers	Ovary	ovary
5	chr6:161399200-161400400	Enhancers	HSMM	muscle
6	chr6:161399200-161401000	Enhancers	HSMMtube	muscle
7	chr6:161399400-161404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:161399600-161400400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:161399600-161400400	Enhancers	Osteobl	bone
10	chr6:161399600-161401000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr6:161399800-161400600	Enhancers	Colon Smooth Muscle	Colon
12	chr6:161399800-161404000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:161400000-161400400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:161400000-161400400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:161400000-161400400	Enhancers	Fetal Intestine Small	intestine
16	chr6:161400000-161400600	Enhancers	Fetal Stomach	stomach
17	chr6:161400000-161400800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:161400000-161400800	Enhancers	Fetal Lung	lung
19	chr6:161400200-161400600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:161400200-161401000	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links