Variant report

Variant	rs2569854
Chromosome Location	chr6:1686068-1686069
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1612762..1614490-chr6:1684651..1686337,2	MCF-7	breast:
2	chr6:1607133..1612092-chr6:1684732..1690668,9	MCF-7	breast:
3	chr6:1685631..1688598-chr6:1691274..1692793,2	MCF-7	breast:
4	chr6:1605266..1613695-chr6:1683912..1689235,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12527698	0.81[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs13202648	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13202650	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17134145	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1962132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2492844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2492845	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2569850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2814817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34826710	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35795009	0.83[EUR][1000 genomes]
rs4323354	1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4357177	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4538753	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4959145	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs4959146	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59679026	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6909257	0.86[AMR][1000 genomes]
rs6931095	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs72838820	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72838830	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9392318	0.87[ASN][1000 genomes]
rs9405503	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9501757	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9502996	0.81[EUR][1000 genomes]
rs9647653	0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
10	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
11	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
12	nsv1015682	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv538092	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1667800-1687800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:1677800-1686200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:1678800-1688000	Weak transcription	Spleen	Spleen
4	chr6:1679400-1693600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:1679600-1695600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:1679600-1715600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:1681600-1686200	Weak transcription	Gastric	stomach
8	chr6:1681600-1699200	Weak transcription	Pancreas	Pancrea
9	chr6:1683000-1698600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:1685000-1687400	Weak transcription	HepG2	liver
11	chr6:1685200-1686200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:1685400-1688000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:1685600-1686200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:1685600-1686200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:1685800-1686200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:1685800-1686200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:1685800-1686200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:1685800-1686200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:1685800-1686200	Enhancers	NH-A	brain
20	chr6:1685800-1686400	Enhancers	Right Atrium	heart
21	chr6:1685800-1686600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:1685800-1686600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr6:1685800-1686600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:1685800-1686600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:1685800-1686600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:1685800-1686800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:1685800-1686800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:1685800-1686800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:1685800-1686800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:1685800-1686800	Enhancers	Esophagus	oesophagus
31	chr6:1685800-1686800	Enhancers	Fetal Muscle Trunk	muscle
32	chr6:1685800-1686800	Enhancers	Ovary	ovary
33	chr6:1685800-1686800	Enhancers	Psoas Muscle	Psoas
34	chr6:1685800-1686800	Flanking Active TSS	Osteobl	bone
35	chr6:1685800-1687000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:1685800-1687000	Enhancers	Fetal Heart	heart
37	chr6:1685800-1687000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:1685800-1687200	Flanking Active TSS	NHEK	skin
39	chr6:1685800-1687600	Enhancers	Left Ventricle	heart
40	chr6:1685800-1687600	Enhancers	HSMM	muscle
41	chr6:1685800-1687600	Enhancers	HUVEC	blood vessel
42	chr6:1685800-1687600	Enhancers	NHDF-Ad	bronchial
43	chr6:1685800-1687600	Enhancers	NHLF	lung
44	chr6:1685800-1687800	Enhancers	Fetal Muscle Leg	muscle
45	chr6:1685800-1687800	Enhancers	HSMMtube	muscle
46	chr6:1685800-1688200	Enhancers	Right Ventricle	heart
47	chr6:1685800-1688400	Enhancers	Lung	lung
48	chr6:1685800-1690000	Enhancers	HMEC	breast
49	chr6:1685800-1690400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:1686000-1686800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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