Variant report

Variant	rs344082
Chromosome Location	chr3:156556079-156556080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156391465..156393079-chr3:156555230..156557059,2	MCF-7	breast:
2	chr3:156404124..156405692-chr3:156554376..156556285,2	K562	blood:
3	chr3:156552175..156554345-chr3:156554997..156556879,2	MCF-7	breast:
4	chr3:156554023..156556645-chr3:156558836..156560959,2	MCF-7	breast:
5	chr3:156541425..156545674-chr3:156551760..156556464,6	K562	blood:

Variant related genes	Relation type
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10212230	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs10936040	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs10936043	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11914959	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12487360	1.00[YRI][hapmap]
rs12491708	1.00[YRI][hapmap]
rs12634915	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs12638253	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs13070271	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13088978	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs1319418	1.00[CEU][hapmap]
rs1320011	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1384538	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1574980	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1995425	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2054880	0.83[JPT][hapmap]
rs2321290	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2321291	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2321292	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2321293	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2321455	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2874488	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2874494	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs2874495	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs343994	0.84[JPT][hapmap]
rs344073	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs344079	1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs344080	1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs344084	1.00[CEU][hapmap];0.94[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];0.99[ASN][1000 genomes]
rs344087	1.00[CEU][hapmap];0.94[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];0.94[ASN][1000 genomes]
rs3910072	0.80[ASN][1000 genomes]
rs416600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234316	1.00[CEU][hapmap]
rs4315647	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs453219	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680311	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680312	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs4680313	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4680314	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680317	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs6441101	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6762708	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6765353	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780427	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs6780475	0.81[EUR][1000 genomes]
rs6783162	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784421	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs6803064	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7615304	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs7622309	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637701	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7638330	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7638625	0.88[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs873337	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9814813	0.88[CHB][hapmap]
rs9826073	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9837038	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs9844054	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs9847187	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs9862338	0.83[EUR][1000 genomes]
rs9863643	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9865905	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs9867621	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9870137	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9871817	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9876010	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs9876148	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs987724	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs9878585	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs9882009	0.81[EUR][1000 genomes]
rs9883439	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs344082	LINC00886	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:156554000-156558200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:156554400-156558400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:156554400-156561000	Weak transcription	Aorta	Aorta
6	chr3:156555200-156556800	Enhancers	HepG2	liver
7	chr3:156555400-156558800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:156555400-156560400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:156555400-156560400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:156555400-156560400	Weak transcription	Osteobl	bone
11	chr3:156555400-156560800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:156555600-156556400	Enhancers	Fetal Intestine Small	intestine
13	chr3:156555600-156556800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:156555600-156560600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:156555600-156560600	Weak transcription	NHDF-Ad	bronchial
16	chr3:156555800-156556800	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links