Variant report

Variant	rs5953643
Chromosome Location	chrX:138852779-138852780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12687833	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12688014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12688450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12688688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12688705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12689199	1.00[GIH][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1361155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs17281969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17281990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17282067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328647	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs17328703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2183251	1.00[CHB][hapmap]
rs2252290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2485721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2485722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap]
rs2485724	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs2485728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485729	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2491005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2491006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap]
rs2491009	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];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs2497266	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];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2497273	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2497274	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs2497277	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2497281	1.00[CHB][hapmap]
rs2497282	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs2497284	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];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2772194	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];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs2805901	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];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4239992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4363374	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs4824924	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs5908669	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];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs5908746	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[YRI][hapmap]
rs5953621	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];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs5953748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5953790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6528650	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];1.00[MKK][hapmap];0.95[YRI][hapmap]
rs6528651	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];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap]
rs6654371	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap]
rs7061584	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];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs7885696	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[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][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	nsv532936	chrX:138687855-139384681	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv491760	chrX:138780768-139283477	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138806800-138866800	Weak transcription	Left Ventricle	heart
2	chrX:138807200-138858200	Weak transcription	Primary B cells from cord blood	blood
3	chrX:138814000-138883600	Weak transcription	Gastric	stomach
4	chrX:138815800-138854200	Weak transcription	Thymus	Thymus
5	chrX:138818600-138857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chrX:138821000-138854600	Weak transcription	Ovary	ovary
7	chrX:138821400-138854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chrX:138821400-138870800	Weak transcription	HSMMtube	muscle
9	chrX:138822000-138857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chrX:138822200-138882600	Weak transcription	Osteobl	bone
11	chrX:138822400-138854400	Weak transcription	HSMM	muscle
12	chrX:138824800-138870000	Weak transcription	Colonic Mucosa	Colon
13	chrX:138826000-138854000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chrX:138827000-138895400	Weak transcription	Hela-S3	cervix
15	chrX:138827400-138888800	Weak transcription	Small Intestine	intestine
16	chrX:138829600-138859200	Weak transcription	HepG2	liver
17	chrX:138833000-138907400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chrX:138837200-138854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chrX:138837400-138853000	Weak transcription	Adipose Nuclei	Adipose
20	chrX:138837400-138855400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chrX:138840600-138854200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chrX:138841000-138870000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chrX:138841400-138854200	Weak transcription	Fetal Stomach	stomach
24	chrX:138841400-138882600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chrX:138841800-138898600	Weak transcription	HUVEC	blood vessel
26	chrX:138842000-138854200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chrX:138842200-138852800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chrX:138842800-138879600	Weak transcription	Brain Germinal Matrix	brain
29	chrX:138843600-138853400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chrX:138844400-138854600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chrX:138844800-138857000	Weak transcription	Stomach Smooth Muscle	stomach
32	chrX:138844800-138881400	Weak transcription	Brain Hippocampus Middle	brain
33	chrX:138845000-138855400	Weak transcription	K562	blood
34	chrX:138845200-138855400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chrX:138845400-138870400	Weak transcription	NH-A	brain
36	chrX:138845800-138857800	Weak transcription	Spleen	Spleen
37	chrX:138847600-138853800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chrX:138847600-138855800	Weak transcription	NHDF-Ad	bronchial
39	chrX:138847600-138875800	Weak transcription	Fetal Kidney	kidney
40	chrX:138847800-138852800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chrX:138847800-138854200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chrX:138847800-138854400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chrX:138847800-138855400	Weak transcription	Dnd41	blood
44	chrX:138847800-138888600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chrX:138847800-138899400	Weak transcription	Aorta	Aorta
46	chrX:138848000-138854200	Weak transcription	Fetal Brain Female	brain
47	chrX:138848000-138870000	Weak transcription	Fetal Lung	lung
48	chrX:138848400-138883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chrX:138848600-138854000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chrX:138848600-138867000	Weak transcription	Rectal Mucosa Donor 29	rectum

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