Variant report

Variant	rs5965003
Chromosome Location	chrX:64912303-64912304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:64908005..64912396-chrX:64917235..64920409,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12387998	0.82[YRI][hapmap]
rs12397033	1.00[MEX][hapmap]
rs16989666	1.00[MEX][hapmap]
rs16989770	1.00[GIH][hapmap]
rs2038284	1.00[MEX][hapmap]
rs2038285	1.00[MEX][hapmap]
rs5964443	1.00[MEX][hapmap]
rs5964999	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs5965004	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs5965006	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs5965007	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs5965030	0.85[ASW][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs6524991	1.00[MEX][hapmap]
rs6525004	1.00[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[YRI][hapmap]
rs6525006	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6525007	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6624812	1.00[ASW][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs6624823	1.00[MEX][hapmap]
rs7050457	0.94[YRI][hapmap]
rs7050592	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7051717	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7058831	1.00[YRI][hapmap]
rs7061281	1.00[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs7062766	0.88[YRI][hapmap]
rs7877834	0.82[YRI][hapmap]
rs7887261	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817451	chrX:64049597-64916072	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv3429625	chrX:64787230-65458721	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv869900	chrX:64885384-64942167	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:64889400-64917200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chrX:64889800-64916600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chrX:64889800-64917000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chrX:64894000-64916400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chrX:64894800-64916000	Weak transcription	Fetal Lung	lung
6	chrX:64894800-64917200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chrX:64900000-64916800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chrX:64903200-64912600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chrX:64903600-64915800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chrX:64903600-64917200	Enhancers	Primary B cells from peripheral blood	blood
11	chrX:64904000-64913800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chrX:64904000-64917000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chrX:64904000-64921000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chrX:64905000-64912400	Enhancers	Osteobl	bone
15	chrX:64906000-64912400	Enhancers	Muscle Satellite Cultured Cells	--
16	chrX:64906600-64915600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chrX:64906600-64917400	Enhancers	HUVEC	blood vessel
18	chrX:64906800-64914000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chrX:64907000-64917000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chrX:64907200-64914000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chrX:64907400-64912400	Genic enhancers	Dnd41	blood
22	chrX:64907600-64914400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chrX:64907800-64914200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chrX:64908000-64915800	Weak transcription	Small Intestine	intestine
25	chrX:64908400-64926800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chrX:64909000-64912600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chrX:64909200-64914600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chrX:64909400-64915400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chrX:64909800-64912400	Enhancers	K562	blood
30	chrX:64910200-64914400	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chrX:64910400-64914200	Weak transcription	Fetal Thymus	thymus
32	chrX:64910400-64914600	Weak transcription	Rectal Smooth Muscle	rectum
33	chrX:64910400-64915400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chrX:64910400-64917000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chrX:64910400-64917200	Weak transcription	A549	lung
36	chrX:64910600-64914600	Weak transcription	Colonic Mucosa	Colon
37	chrX:64910600-64916000	Weak transcription	Liver	Liver
38	chrX:64910600-64916000	Weak transcription	Brain Substantia Nigra	brain
39	chrX:64910600-64917000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chrX:64910600-64918200	Weak transcription	Pancreas	Pancrea
41	chrX:64910800-64913000	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chrX:64910800-64914000	Weak transcription	Fetal Heart	heart
43	chrX:64910800-64914200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chrX:64910800-64914400	Weak transcription	Fetal Muscle Trunk	muscle
45	chrX:64910800-64914400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chrX:64910800-64914400	Weak transcription	NHLF	lung
47	chrX:64910800-64916200	Enhancers	Primary B cells from cord blood	blood
48	chrX:64910800-64923600	Weak transcription	Brain Cingulate Gyrus	brain
49	chrX:64910800-64926000	Weak transcription	Esophagus	oesophagus
50	chrX:64911000-64913400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links