Variant report

Variant	rs5942897
Chromosome Location	chrX:109368709-109368710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:109246026..109248480-chrX:109367348..109370363,3	MCF-7	breast:
2	chrX:109289458..109289966-chrX:109368509..109369222,2	MCF-7	breast:
3	chrX:109158405..109158926-chrX:109368381..109369147,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157600	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11152597	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs11797230	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs12841904	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1418393	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs1623948	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1770343	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap]
rs1774690	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1774691	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2066364	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2791640	0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2795991	0.85[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap]
rs2795992	0.85[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap]
rs2795993	0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2795994	0.85[ASW][hapmap];0.93[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap]
rs2881449	0.88[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap]
rs34247395	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4081383	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs4421522	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]
rs4628434	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs4893450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs5942620	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942626	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs5942628	0.85[ASW][hapmap];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];0.94[YRI][hapmap]
rs5942629	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs5942880	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs5942883	0.88[CHB][hapmap];0.83[GIH][hapmap]
rs5942886	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942887	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5942890	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];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs5942896	0.85[ASW][hapmap];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];0.94[YRI][hapmap]
rs5985271	0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[MEX][hapmap]
rs5985439	0.88[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap]
rs5985440	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5985442	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs5985446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs6567845	0.89[LWK][hapmap]
rs946820	0.86[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap]
rs946821	0.86[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs946822	0.86[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap]
rs947592	0.85[CHD][hapmap];0.88[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109267200-109377800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chrX:109331200-109382400	Weak transcription	Right Ventricle	heart
3	chrX:109334000-109402600	Weak transcription	Primary B cells from cord blood	blood
4	chrX:109346800-109378000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chrX:109350200-109368800	Weak transcription	Psoas Muscle	Psoas
6	chrX:109350200-109374600	Weak transcription	Esophagus	oesophagus
7	chrX:109350200-109385200	Weak transcription	Pancreas	Pancrea
8	chrX:109350800-109371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chrX:109351600-109380200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chrX:109352400-109402400	Weak transcription	Primary B cells from peripheral blood	blood
11	chrX:109352400-109414000	Weak transcription	Dnd41	blood
12	chrX:109353000-109368800	Weak transcription	Left Ventricle	heart
13	chrX:109353000-109375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chrX:109353200-109389000	Weak transcription	Hela-S3	cervix
15	chrX:109354200-109376800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chrX:109354200-109382400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chrX:109355000-109370800	Weak transcription	Ovary	ovary
18	chrX:109356400-109377200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chrX:109358000-109382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chrX:109363400-109377000	Weak transcription	K562	blood
21	chrX:109363600-109375000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chrX:109363600-109392600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chrX:109363800-109376800	Weak transcription	A549	lung
24	chrX:109364200-109376800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chrX:109364600-109369800	Weak transcription	Primary hematopoietic stem cells	blood
26	chrX:109365400-109373800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chrX:109366800-109368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chrX:109367200-109396200	Weak transcription	Duodenum Mucosa	Duodenum
29	chrX:109367800-109370000	Weak transcription	HepG2	liver
30	chrX:109367800-109389200	Weak transcription	Fetal Intestine Large	intestine
31	chrX:109368000-109368800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chrX:109368000-109369800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chrX:109368000-109378400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chrX:109368400-109368800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chrX:109368400-109369000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chrX:109368400-109385200	Weak transcription	Brain Anterior Caudate	brain
37	chrX:109368600-109368800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chrX:109368600-109369000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chrX:109368600-109369400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chrX:109368600-109369600	Strong transcription	Fetal Intestine Small	intestine
41	chrX:109368600-109370200	Enhancers	Fetal Heart	heart
42	chrX:109368600-109370400	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chrX:109368600-109371600	Enhancers	Skeletal Muscle Female	skeletal muscle

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