Variant report

Variant	rs3800032
Chromosome Location	chr6:1737097-1737098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1728980..1730810-chr6:1735730..1738252,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1013303	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1040530	0.81[JPT][hapmap]
rs10458130	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12197874	0.87[EUR][1000 genomes]
rs12200248	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs12208162	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12529650	0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs34669469	0.87[ASN][1000 genomes]
rs3734739	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3734740	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3800034	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3800035	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3800036	0.88[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs3800037	0.85[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs3800038	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3800040	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800043	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs3823262	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4140588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4546532	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4959605	0.81[JPT][hapmap]
rs56046637	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62388352	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6596850	0.94[EUR][1000 genomes]
rs6912189	0.96[EUR][1000 genomes]
rs6914704	0.89[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs6916153	0.84[EUR][1000 genomes]
rs6920971	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6933551	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6934958	0.83[EUR][1000 genomes]
rs742536	0.89[CEU][hapmap]
rs761148	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9392332	0.82[CHB][hapmap];0.81[JPT][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	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv600809	chr6:1732741-1775436	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3333870	chr6:1735853-1740251	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv3399950	chr6:1735853-1740351	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
2	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:1721200-1746200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:1721200-1748800	Weak transcription	Osteobl	bone
5	chr6:1721400-1739400	Weak transcription	Hela-S3	cervix
6	chr6:1723000-1743200	Strong transcription	HepG2	liver
7	chr6:1725000-1737800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:1726800-1749000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:1726800-1749000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:1727000-1737600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:1731800-1745000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:1731800-1746200	Weak transcription	Right Atrium	heart
13	chr6:1732200-1744800	Weak transcription	Aorta	Aorta
14	chr6:1732200-1750600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:1732200-1756600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:1735800-1738000	Weak transcription	Spleen	Spleen
17	chr6:1735800-1741600	Weak transcription	Fetal Intestine Small	intestine
18	chr6:1736000-1737600	Weak transcription	Gastric	stomach
19	chr6:1736000-1737800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:1736000-1737800	Weak transcription	Pancreas	Pancrea
21	chr6:1736000-1746200	Weak transcription	Esophagus	oesophagus
22	chr6:1736000-1746200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:1736400-1739200	Enhancers	GM12878-XiMat	blood
24	chr6:1736400-1746200	Weak transcription	Right Ventricle	heart
25	chr6:1737000-1737200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:1737000-1737200	Enhancers	Primary B cells from peripheral blood	blood
27	chr6:1737000-1737200	Enhancers	Brain Germinal Matrix	brain
28	chr6:1737000-1749000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links