Variant report

Variant	rs5942886
Chromosome Location	chrX:109324607-109324608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGAG1-3	chrX:109324070-109325388	ncRnaDb_ncrna_FR214632_1

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];0.89[MKK][hapmap];0.96[TSI][hapmap];0.81[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];0.96[TSI][hapmap]
rs12841904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.96[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];0.96[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]
rs2795994	1.00[JPT][hapmap]
rs2881449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs34247395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.87[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];0.96[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];0.96[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];0.96[TSI][hapmap]
rs5942887	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];0.96[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];0.96[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];0.96[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:34 , 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:109280200-109331800	Weak transcription	Primary B cells from cord blood	blood
3	chrX:109289200-109325000	Weak transcription	Psoas Muscle	Psoas
4	chrX:109297000-109324800	Weak transcription	Fetal Thymus	thymus
5	chrX:109304400-109328600	Weak transcription	Hela-S3	cervix
6	chrX:109305000-109325000	Weak transcription	HSMM	muscle
7	chrX:109305000-109330200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chrX:109307600-109329400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chrX:109311000-109328800	Weak transcription	Left Ventricle	heart
10	chrX:109311800-109329000	Weak transcription	Duodenum Mucosa	Duodenum
11	chrX:109316800-109329000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chrX:109316800-109329000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chrX:109317200-109324800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chrX:109317200-109329000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chrX:109317600-109329400	Weak transcription	Primary hematopoietic stem cells	blood
16	chrX:109318200-109325000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chrX:109319400-109328800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chrX:109320200-109328800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chrX:109321400-109325000	Weak transcription	Brain Anterior Caudate	brain
20	chrX:109323000-109324800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chrX:109323400-109326200	Enhancers	HMEC	breast
22	chrX:109323400-109327600	Enhancers	NHEK	skin
23	chrX:109324200-109331000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chrX:109324400-109324800	Weak transcription	Fetal Intestine Small	intestine
25	chrX:109324400-109326200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chrX:109324400-109326800	Enhancers	HUVEC	blood vessel
27	chrX:109324600-109325200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chrX:109324600-109325200	Enhancers	A549	lung
29	chrX:109324600-109325400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chrX:109324600-109325800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chrX:109324600-109326000	Enhancers	Fetal Heart	heart
32	chrX:109324600-109326000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chrX:109324600-109326600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chrX:109324600-109327200	Enhancers	Muscle Satellite Cultured Cells	--

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