Variant report

Variant	rs2569862
Chromosome Location	chr6:1640551-1640552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1639221..1644063-chr6:1670120..1672806,4	MCF-7	breast:
2	chr6:1640135..1642323-chr6:1758348..1760880,2	MCF-7	breast:
3	chr6:1639353..1642939-chr6:1657811..1662658,4	MCF-7	breast:
4	chr6:1608387..1612062-chr6:1640147..1644429,6	MCF-7	breast:
5	chr6:1638763..1640765-chr6:1680468..1682167,2	MCF-7	breast:
6	chr6:1640395..1643139-chr6:1772426..1774181,2	MCF-7	breast:
7	chr6:1640459..1644974-chr6:1686187..1689863,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10214732	0.92[JPT][hapmap]
rs11242715	0.92[JPT][hapmap]
rs12192836	0.92[JPT][hapmap]
rs12203057	0.92[JPT][hapmap]
rs1810496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007297	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569856	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569857	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2569859	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4461777	0.85[JPT][hapmap]
rs4959144	0.92[JPT][hapmap]
rs7759035	0.92[JPT][hapmap]
rs910019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9501754	0.92[JPT][hapmap]
rs9501755	0.92[JPT][hapmap]
rs9501758	0.92[JPT][hapmap]
rs9501759	0.84[JPT][hapmap]
rs9502997	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	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
7	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	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
11	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2569862	C6orf195	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1631600-1646000	Weak transcription	Osteobl	bone
2	chr6:1633000-1679800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:1634200-1644000	Strong transcription	HepG2	liver
4	chr6:1634400-1648600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:1634600-1643400	Weak transcription	Spleen	Spleen
6	chr6:1636200-1641400	Weak transcription	HUVEC	blood vessel
7	chr6:1636800-1657200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:1637600-1641400	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:1637600-1641400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:1637600-1641600	Weak transcription	Fetal Intestine Large	intestine
11	chr6:1637600-1643600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:1637800-1641400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:1637800-1643000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:1637800-1646200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:1638000-1641200	Weak transcription	Hela-S3	cervix
16	chr6:1638000-1641600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:1638000-1644200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:1638200-1641000	Weak transcription	HMEC	breast
19	chr6:1638200-1641200	Weak transcription	Stomach Mucosa	stomach
20	chr6:1638400-1641200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:1638400-1641200	Weak transcription	NHEK	skin
22	chr6:1638400-1641400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:1638400-1641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:1638600-1640600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:1639000-1641800	Strong transcription	Primary T cells from cord blood	blood
26	chr6:1639200-1641000	Strong transcription	Gastric	stomach
27	chr6:1639200-1641200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:1639200-1642000	Strong transcription	Fetal Intestine Small	intestine
29	chr6:1639400-1640600	Strong transcription	Colonic Mucosa	Colon
30	chr6:1639800-1640600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:1639800-1640800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:1640200-1640800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr6:1640200-1642400	Enhancers	Pancreas	Pancrea
34	chr6:1640200-1642600	Enhancers	Placenta	Placenta
35	chr6:1640400-1640600	Enhancers	Lung	lung
36	chr6:1640400-1641600	Enhancers	Esophagus	oesophagus

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