Variant report

Variant	rs9378643
Chromosome Location	chr6:1646520-1646521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1646158..1647833-chr6:1681019..1683141,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12197376	0.95[JPT][hapmap]
rs12210324	0.95[JPT][hapmap]
rs1962433	0.95[JPT][hapmap]
rs2246345	0.95[JPT][hapmap]
rs2317964	0.95[JPT][hapmap]
rs2569832	0.87[JPT][hapmap]
rs2569842	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2569844	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs2569846	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569847	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2569848	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2569879	0.86[JPT][hapmap]
rs2745564	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs2814806	0.87[JPT][hapmap]
rs2814807	0.86[JPT][hapmap]
rs2814808	0.87[JPT][hapmap]
rs2814809	1.00[JPT][hapmap]
rs2814813	0.95[JPT][hapmap]
rs2814816	0.82[JPT][hapmap]
rs2814820	0.90[JPT][hapmap]
rs2814827	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4060649	0.95[JPT][hapmap]
rs4552776	0.95[JPT][hapmap]
rs4959586	0.86[JPT][hapmap]
rs62390650	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6905377	0.91[JPT][hapmap]
rs6913557	0.95[JPT][hapmap]
rs6916770	0.95[JPT][hapmap]
rs6917693	0.95[JPT][hapmap]
rs6930694	0.95[JPT][hapmap]
rs742556	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs742557	0.95[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7757590	0.87[JPT][hapmap]
rs9378303	0.95[JPT][hapmap]
rs9378304	0.95[JPT][hapmap]
rs9378647	0.95[JPT][hapmap]
rs9378648	0.95[JPT][hapmap]
rs9378649	0.95[JPT][hapmap]
rs9392319	0.95[JPT][hapmap]
rs9405144	0.95[JPT][hapmap]
rs9405502	0.95[JPT][hapmap]
rs9501750	0.87[JPT][hapmap]
rs9501751	0.86[JPT][hapmap]
rs9503002	0.95[JPT][hapmap]
rs9647654	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1633000-1679800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:1634400-1648600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:1636800-1657200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:1640600-1649400	Weak transcription	Colonic Mucosa	Colon
5	chr6:1640800-1651200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:1641200-1653000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:1641800-1662800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:1642400-1647800	Weak transcription	Gastric	stomach
9	chr6:1642400-1653000	Weak transcription	Pancreas	Pancrea
10	chr6:1642400-1657200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:1642400-1660800	Weak transcription	Small Intestine	intestine
12	chr6:1643800-1646600	Weak transcription	Fetal Intestine Small	intestine
13	chr6:1643800-1648000	Weak transcription	Spleen	Spleen
14	chr6:1643800-1671200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:1644000-1647800	Weak transcription	HepG2	liver
16	chr6:1644800-1647200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:1645000-1665800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:1645200-1659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:1645800-1647400	Enhancers	Fetal Muscle Leg	muscle
20	chr6:1646000-1646600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:1646000-1646600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:1646000-1646800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:1646000-1646800	Enhancers	Osteobl	bone
24	chr6:1646000-1647200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:1646200-1646600	Enhancers	NHDF-Ad	bronchial
26	chr6:1646200-1647000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:1646200-1647000	Enhancers	NHEK	skin
28	chr6:1646200-1647400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:1646400-1646600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:1646400-1646800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:1646400-1646800	Enhancers	Esophagus	oesophagus
32	chr6:1646400-1646800	Enhancers	HMEC	breast

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