Variant report

Variant	rs6890476
Chromosome Location	chr5:111708480-111708481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:111573916..111574468-chr5:111707850..111708653,3	MCF-7	breast:
2	chr5:111707943..111708524-chr5:111755720..111756286,2	MCF-7	breast:
3	chr5:111707104..111709400-chr5:111753437..111755774,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268358	Chromatin interaction
ENSG00000129595	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10036357	0.92[EUR][1000 genomes]
rs10039730	1.00[JPT][hapmap]
rs10044406	1.00[JPT][hapmap]
rs10051512	1.00[JPT][hapmap]
rs10056040	0.92[EUR][1000 genomes]
rs10059675	1.00[EUR][1000 genomes]
rs10060962	1.00[JPT][hapmap]
rs10061025	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10061207	1.00[JPT][hapmap]
rs10062045	1.00[JPT][hapmap]
rs10068969	1.00[JPT][hapmap]
rs10068974	1.00[JPT][hapmap]
rs10069313	0.92[EUR][1000 genomes]
rs10069608	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10069773	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10071058	1.00[JPT][hapmap]
rs10071862	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10071986	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10072705	1.00[JPT][hapmap]
rs10076627	0.82[EUR][1000 genomes]
rs10077309	0.92[EUR][1000 genomes]
rs10077774	1.00[JPT][hapmap]
rs10477480	0.92[EUR][1000 genomes]
rs10478080	1.00[ASN][1000 genomes]
rs10478081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10478083	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10478084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10515444	1.00[JPT][hapmap]
rs11288564	0.92[EUR][1000 genomes]
rs13354202	1.00[JPT][hapmap]
rs13354699	1.00[JPT][hapmap]
rs13355990	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1524423	1.00[JPT][hapmap]
rs1524424	0.92[EUR][1000 genomes]
rs1554624	1.00[JPT][hapmap]
rs17134423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17134426	1.00[JPT][hapmap]
rs17134429	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17134454	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs17134475	0.92[EUR][1000 genomes]
rs17134478	1.00[JPT][hapmap]
rs17134503	1.00[JPT][hapmap]
rs17134505	1.00[JPT][hapmap]
rs17134521	0.92[EUR][1000 genomes]
rs2416285	1.00[JPT][hapmap]
rs28497526	0.92[EUR][1000 genomes]
rs28631626	0.92[EUR][1000 genomes]
rs28806604	0.92[EUR][1000 genomes]
rs28831993	0.92[EUR][1000 genomes]
rs28836584	0.92[EUR][1000 genomes]
rs28887818	0.92[EUR][1000 genomes]
rs388383	1.00[JPT][hapmap]
rs3985058	1.00[JPT][hapmap]
rs448714	1.00[JPT][hapmap]
rs6594590	1.00[JPT][hapmap]
rs6594594	1.00[JPT][hapmap]
rs6594596	1.00[JPT][hapmap]
rs6594597	0.92[EUR][1000 genomes]
rs6860402	1.00[JPT][hapmap]
rs6863610	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6865127	1.00[JPT][hapmap]
rs6865715	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873453	0.92[EUR][1000 genomes]
rs6878092	1.00[JPT][hapmap]
rs6878158	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6879906	1.00[JPT][hapmap]
rs6883585	1.00[JPT][hapmap]
rs6883800	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6884339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6891512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6893840	1.00[JPT][hapmap]
rs6894365	1.00[JPT][hapmap]
rs6895299	0.92[EUR][1000 genomes]
rs721054	1.00[JPT][hapmap]
rs721055	1.00[JPT][hapmap]
rs73214254	0.92[EUR][1000 genomes]
rs73214256	0.92[EUR][1000 genomes]
rs73218338	0.92[EUR][1000 genomes]
rs73218343	0.92[EUR][1000 genomes]
rs7702999	1.00[JPT][hapmap]
rs7705094	0.92[EUR][1000 genomes]
rs7706551	1.00[JPT][hapmap]
rs7706737	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7707028	1.00[JPT][hapmap]
rs7709879	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7709963	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7710041	1.00[JPT][hapmap]
rs7710507	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7711662	0.92[EUR][1000 genomes]
rs7714450	0.84[EUR][1000 genomes]
rs7725728	1.00[JPT][hapmap]
rs7730739	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7733415	1.00[JPT][hapmap]
rs7736305	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7736457	0.92[EUR][1000 genomes]
rs9326853	1.00[JPT][hapmap]
rs985873	1.00[JPT][hapmap]
rs986797	1.00[JPT][hapmap]
rs9885137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9885177	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885182	1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885209	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885211	1.00[EUR][1000 genomes]
rs9885390	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs999243	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	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111685200-111709800	Weak transcription	Aorta	Aorta
2	chr5:111689600-111708800	Weak transcription	Esophagus	oesophagus
3	chr5:111701600-111712200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:111703400-111708800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:111704400-111726000	Weak transcription	Lung	lung
6	chr5:111705000-111709200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:111705600-111710800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:111705600-111714600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:111705800-111708800	Weak transcription	Right Atrium	heart
10	chr5:111705800-111709800	Weak transcription	Right Ventricle	heart
11	chr5:111706600-111711800	Enhancers	Fetal Heart	heart
12	chr5:111707400-111708800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:111707400-111708800	Weak transcription	Left Ventricle	heart
14	chr5:111707400-111709000	Weak transcription	Gastric	stomach
15	chr5:111707400-111714600	Weak transcription	Ovary	ovary
16	chr5:111707400-111726000	Weak transcription	Pancreas	Pancrea
17	chr5:111708400-111725600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links