Variant report

Variant	rs5942880
Chromosome Location	chrX:109285322-109285323
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:109247919..109249928-chrX:109284339..109286219,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11152597	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11797230	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12841904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1418393	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1774691	1.00[JPT][hapmap]
rs2066364	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2791640	1.00[JPT][hapmap]
rs2795991	1.00[JPT][hapmap]
rs2795992	1.00[JPT][hapmap]
rs2795993	1.00[JPT][hapmap]
rs2881449	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs34247395	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4081383	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4421522	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4628434	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4893450	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs5942620	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5942626	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs5942628	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs5942629	0.88[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap]
rs5942883	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs5942886	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5942887	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5942890	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs5942896	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs5942897	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs5985271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs5985439	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5985440	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5985442	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs5985446	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs947592	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109246800-109294000	Weak transcription	Primary T cells from cord blood	blood
2	chrX:109247400-109318200	Weak transcription	Thymus	Thymus
3	chrX:109248600-109310200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chrX:109251000-109286200	Weak transcription	Primary hematopoietic stem cells	blood
5	chrX:109265400-109292600	Weak transcription	Aorta	Aorta
6	chrX:109266600-109318000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chrX:109267200-109377800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chrX:109270000-109290000	Weak transcription	Right Ventricle	heart
9	chrX:109270200-109311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chrX:109270800-109288000	Weak transcription	Right Atrium	heart
11	chrX:109273000-109286800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chrX:109273200-109310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chrX:109276000-109285400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chrX:109276200-109288600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chrX:109276200-109291200	Weak transcription	Brain Angular Gyrus	brain
16	chrX:109276200-109295400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chrX:109280000-109286600	Weak transcription	K562	blood
18	chrX:109280200-109331800	Weak transcription	Primary B cells from cord blood	blood
19	chrX:109280400-109286200	Weak transcription	Small Intestine	intestine
20	chrX:109280400-109316600	Weak transcription	Primary B cells from peripheral blood	blood
21	chrX:109280600-109304600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chrX:109280600-109310200	Weak transcription	Duodenum Mucosa	Duodenum
23	chrX:109280800-109285600	Weak transcription	Adipose Nuclei	Adipose
24	chrX:109280800-109286000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chrX:109280800-109288600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chrX:109280800-109288600	Weak transcription	Pancreas	Pancrea
27	chrX:109280800-109289400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chrX:109281000-109286200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chrX:109281800-109296400	Weak transcription	Left Ventricle	heart
30	chrX:109282000-109288000	Weak transcription	Fetal Intestine Small	intestine
31	chrX:109282000-109297800	Weak transcription	Fetal Intestine Large	intestine
32	chrX:109282000-109297800	Weak transcription	Gastric	stomach
33	chrX:109282400-109286600	Enhancers	Fetal Heart	heart
34	chrX:109282600-109285400	Weak transcription	Hela-S3	cervix
35	chrX:109282800-109288800	Weak transcription	Psoas Muscle	Psoas
36	chrX:109282800-109290600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chrX:109282800-109304600	Weak transcription	Brain Hippocampus Middle	brain
38	chrX:109283200-109285800	Weak transcription	A549	lung
39	chrX:109283200-109286800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chrX:109283200-109290800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chrX:109283600-109286800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chrX:109284000-109318200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chrX:109284200-109286600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chrX:109284200-109288800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chrX:109284200-109292600	Weak transcription	Brain Anterior Caudate	brain
46	chrX:109284400-109285600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chrX:109284400-109288200	Enhancers	Primary monocytes fromperipheralblood	blood
48	chrX:109285200-109287400	Enhancers	Primary neutrophils fromperipheralblood	blood

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