Variant report

Variant	rs5942887
Chromosome Location	chrX:109325486-109325487
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	chrX:109194429..109197002-chrX:109325433..109327043,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11152597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs11797230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs12841904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1418393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs1623948	1.00[JPT][hapmap]
rs1770343	1.00[JPT][hapmap]
rs1774690	1.00[JPT][hapmap]
rs2066364	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[TSI][hapmap]
rs2795994	1.00[JPT][hapmap]
rs2881449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs34247395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs4081383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs4421522	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs4628434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4893450	0.88[CHB][hapmap]
rs5942620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs5942626	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942628	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942629	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs5942880	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5942883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5942886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap]
rs5942890	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942896	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942897	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5985271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs5985439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5985440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs5985442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs5985446	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs946820	1.00[JPT][hapmap]
rs946821	1.00[JPT][hapmap]
rs946822	1.00[JPT][hapmap]
rs947592	0.88[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531154	chrX:108934095-109332109	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	130 gene(s)	inside rSNPs	diseases
2	esv3369563	chrX:109079631-109573656	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	142 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109267200-109377800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chrX:109280200-109331800	Weak transcription	Primary B cells from cord blood	blood
3	chrX:109304400-109328600	Weak transcription	Hela-S3	cervix
4	chrX:109305000-109330200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chrX:109307600-109329400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chrX:109311000-109328800	Weak transcription	Left Ventricle	heart
7	chrX:109311800-109329000	Weak transcription	Duodenum Mucosa	Duodenum
8	chrX:109316800-109329000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chrX:109316800-109329000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chrX:109317200-109329000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chrX:109317600-109329400	Weak transcription	Primary hematopoietic stem cells	blood
12	chrX:109319400-109328800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chrX:109320200-109328800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chrX:109323400-109326200	Enhancers	HMEC	breast
15	chrX:109323400-109327600	Enhancers	NHEK	skin
16	chrX:109324200-109331000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chrX:109324400-109326200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chrX:109324400-109326800	Enhancers	HUVEC	blood vessel
19	chrX:109324600-109325800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chrX:109324600-109326000	Enhancers	Fetal Heart	heart
21	chrX:109324600-109326000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chrX:109324600-109326600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chrX:109324600-109327200	Enhancers	Muscle Satellite Cultured Cells	--
24	chrX:109324800-109325600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chrX:109324800-109325600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chrX:109324800-109325600	Enhancers	NH-A	brain
27	chrX:109324800-109326000	Enhancers	Right Ventricle	heart
28	chrX:109325000-109325600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
29	chrX:109325000-109325600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
30	chrX:109325000-109325600	Enhancers	Aorta	Aorta
31	chrX:109325000-109325600	Enhancers	Brain Anterior Caudate	brain
32	chrX:109325000-109325600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chrX:109325000-109325600	Weak transcription	Fetal Thymus	thymus
34	chrX:109325000-109325600	Enhancers	Lung	lung
35	chrX:109325000-109325600	Enhancers	Ovary	ovary
36	chrX:109325000-109326000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chrX:109325000-109326000	Enhancers	Brain Hippocampus Middle	brain
38	chrX:109325000-109326000	Enhancers	NHLF	lung
39	chrX:109325000-109326200	Enhancers	HSMM	muscle
40	chrX:109325200-109325600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chrX:109325200-109325600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chrX:109325200-109325600	Enhancers	Colon Smooth Muscle	Colon
43	chrX:109325200-109325800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chrX:109325200-109325800	Flanking Active TSS	A549	lung
45	chrX:109325200-109326000	Enhancers	Brain Substantia Nigra	brain
46	chrX:109325200-109326200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chrX:109325200-109326200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chrX:109325200-109326400	Bivalent Enhancer	Osteobl	bone
49	chrX:109325400-109325800	Weak transcription	Stomach Mucosa	stomach
50	chrX:109325400-109326000	Enhancers	Rectal Smooth Muscle	rectum

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