Variant report

Variant	rs5942620
Chromosome Location	chrX:109291468-109291469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11152597	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs11797230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12841904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1418393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs34247395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4081383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4421522	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs4628434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4893450	0.88[CHB][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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5942886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs5942887	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]
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];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs5985439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5985440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[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:60 , 50 per page) page: 1 2

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:109265400-109292600	Weak transcription	Aorta	Aorta
5	chrX:109266600-109318000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chrX:109267200-109377800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chrX:109270200-109311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chrX:109273200-109310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chrX:109276200-109295400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chrX:109280200-109331800	Weak transcription	Primary B cells from cord blood	blood
11	chrX:109280400-109316600	Weak transcription	Primary B cells from peripheral blood	blood
12	chrX:109280600-109304600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chrX:109280600-109310200	Weak transcription	Duodenum Mucosa	Duodenum
14	chrX:109281800-109296400	Weak transcription	Left Ventricle	heart
15	chrX:109282000-109297800	Weak transcription	Fetal Intestine Large	intestine
16	chrX:109282000-109297800	Weak transcription	Gastric	stomach
17	chrX:109282800-109304600	Weak transcription	Brain Hippocampus Middle	brain
18	chrX:109284000-109318200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chrX:109284200-109292600	Weak transcription	Brain Anterior Caudate	brain
20	chrX:109286400-109304000	Weak transcription	Hela-S3	cervix
21	chrX:109286800-109316600	Weak transcription	Primary hematopoietic stem cells	blood
22	chrX:109287000-109292800	Enhancers	Fetal Heart	heart
23	chrX:109287400-109296400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chrX:109287600-109297000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chrX:109288400-109293400	Weak transcription	Ovary	ovary
26	chrX:109288600-109312800	Weak transcription	Fetal Intestine Small	intestine
27	chrX:109288800-109295800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chrX:109289000-109295200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chrX:109289200-109292000	Weak transcription	Right Atrium	heart
30	chrX:109289200-109292200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chrX:109289200-109325000	Weak transcription	Psoas Muscle	Psoas
32	chrX:109289400-109292800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chrX:109289400-109294000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chrX:109289800-109292600	Weak transcription	Pancreas	Pancrea
35	chrX:109289800-109296600	Weak transcription	Fetal Thymus	thymus
36	chrX:109290000-109298600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chrX:109290200-109291800	Active TSS	Right Ventricle	heart
38	chrX:109290200-109291800	Strong transcription	K562	blood
39	chrX:109290200-109292600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chrX:109290200-109293000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chrX:109290200-109293400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chrX:109290400-109294200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chrX:109290400-109294600	Weak transcription	A549	lung
44	chrX:109290600-109292800	Weak transcription	GM12878-XiMat	blood
45	chrX:109290800-109292800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chrX:109290800-109292800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chrX:109290800-109294600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chrX:109290800-109295600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chrX:109290800-109296600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chrX:109291000-109291600	Enhancers	Primary monocytes fromperipheralblood	blood

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