Variant report

Variant	rs1623948
Chromosome Location	chrX:109385817-109385818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11152597	1.00[JPT][hapmap]
rs11797230	1.00[JPT][hapmap]
rs1418393	1.00[JPT][hapmap]
rs1770343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs1774690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1774691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2791640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2795991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs2795992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs2795993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2795994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2795995	0.87[CHB][hapmap]
rs2881449	1.00[JPT][hapmap]
rs4081383	1.00[JPT][hapmap]
rs4421522	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap]
rs4628434	1.00[JPT][hapmap]
rs4893450	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs5942620	1.00[JPT][hapmap]
rs5942626	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs5942628	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap]
rs5942629	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs5942883	1.00[JPT][hapmap]
rs5942886	1.00[JPT][hapmap]
rs5942887	1.00[JPT][hapmap]
rs5942890	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs5942896	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap]
rs5942897	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs5942899	0.87[CHB][hapmap]
rs5985271	1.00[JPT][hapmap]
rs5985439	1.00[JPT][hapmap]
rs5985440	1.00[JPT][hapmap]
rs5985442	1.00[JPT][hapmap]
rs5985446	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs946820	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs946821	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs946822	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109334000-109402600	Weak transcription	Primary B cells from cord blood	blood
2	chrX:109352400-109402400	Weak transcription	Primary B cells from peripheral blood	blood
3	chrX:109352400-109414000	Weak transcription	Dnd41	blood
4	chrX:109353200-109389000	Weak transcription	Hela-S3	cervix
5	chrX:109363600-109392600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chrX:109367200-109396200	Weak transcription	Duodenum Mucosa	Duodenum
7	chrX:109367800-109389200	Weak transcription	Fetal Intestine Large	intestine
8	chrX:109369600-109388200	Weak transcription	Fetal Intestine Small	intestine
9	chrX:109369800-109387800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chrX:109371000-109386000	Weak transcription	Ovary	ovary
11	chrX:109373600-109388600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chrX:109374000-109389200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chrX:109374400-109389400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chrX:109375600-109389400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chrX:109376800-109392000	Weak transcription	Primary T cells from cord blood	blood
16	chrX:109377400-109388800	Weak transcription	A549	lung
17	chrX:109377600-109403400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chrX:109378000-109392400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chrX:109379000-109387000	Weak transcription	Colonic Mucosa	Colon
20	chrX:109381000-109386200	Weak transcription	Fetal Heart	heart
21	chrX:109382600-109387000	Weak transcription	Psoas Muscle	Psoas
22	chrX:109382600-109389200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chrX:109382800-109388000	Weak transcription	Placenta	Placenta
24	chrX:109382800-109392600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chrX:109383400-109388800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chrX:109384200-109389800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chrX:109384800-109387800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chrX:109384800-109387800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chrX:109384800-109389600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chrX:109384800-109390400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chrX:109385000-109387200	Enhancers	HMEC	breast
32	chrX:109385000-109388200	Enhancers	NHEK	skin
33	chrX:109385200-109386200	Enhancers	Right Atrium	heart
34	chrX:109385200-109386400	Enhancers	Pancreas	Pancrea
35	chrX:109385200-109386400	Enhancers	Spleen	Spleen
36	chrX:109385200-109386600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chrX:109385200-109386800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chrX:109385200-109387000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chrX:109385200-109387400	Enhancers	Esophagus	oesophagus
40	chrX:109385200-109390000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chrX:109385400-109386200	Enhancers	Left Ventricle	heart
42	chrX:109385400-109386400	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chrX:109385400-109387000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chrX:109385400-109387200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chrX:109385600-109386400	Bivalent Enhancer	Osteobl	bone
46	chrX:109385600-109386800	Weak transcription	Lung	lung
47	chrX:109385600-109387200	Enhancers	Adipose Nuclei	Adipose
48	chrX:109385600-109388600	Weak transcription	Brain Anterior Caudate	brain
49	chrX:109385600-109388600	Weak transcription	K562	blood
50	chrX:109385600-109389200	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links