Variant report

Variant	rs5964500
Chromosome Location	chrX:65414617-65414618
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:65240471..65245017-chrX:65410397..65415095,7	K562	blood:
2	chrX:65408173..65411211-chrX:65412672..65415962,4	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1011526	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1028348	0.93[MEX][hapmap]
rs1068536	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs1068537	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1068538	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs1090752	0.86[CEU][hapmap]
rs1090842	0.86[CEU][hapmap]
rs1091486	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs12395548	1.00[ASW][hapmap];0.83[GIH][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs1264212	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1264216	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1264218	1.00[CEU][hapmap]
rs1325561	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs13440529	0.84[CEU][hapmap]
rs1415297	0.83[GIH][hapmap]
rs1456803	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs1456804	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1456806	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs17301659	1.00[CEU][hapmap]
rs1989028	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2054179	0.86[CEU][hapmap]
rs2198868	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2198869	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2206203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3848901	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs3903921	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3903922	1.00[YRI][hapmap]
rs4827365	0.86[CEU][hapmap]
rs4827449	1.00[ASW][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs585069	0.86[MEX][hapmap]
rs586789	0.86[MEX][hapmap]
rs587657	0.86[MEX][hapmap]
rs5918587	0.86[MEX][hapmap]
rs5918594	0.83[ASW][hapmap];0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs5918974	0.86[MEX][hapmap]
rs5919024	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs5919069	1.00[ASW][hapmap];0.83[GIH][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs5964483	1.00[ASW][hapmap]
rs5964487	1.00[ASW][hapmap]
rs5964488	1.00[ASW][hapmap]
rs5964495	1.00[CEU][hapmap]
rs5964499	1.00[CEU][hapmap]
rs5965105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5965106	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs5965110	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap]
rs606886	0.86[MEX][hapmap]
rs651494	0.86[CEU][hapmap]
rs6624844	0.86[MEX][hapmap]
rs6624875	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs6624876	1.00[CEU][hapmap]
rs670546	0.86[MEX][hapmap]
rs699863	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7054364	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7062799	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs707298	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs707302	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs708966	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs708968	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs708969	0.86[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs760866	1.00[CEU][hapmap]
rs760867	0.91[ASW][hapmap];0.86[MEX][hapmap]
rs7891437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs806538	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs806607	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap]
rs806608	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs806609	1.00[CEU][hapmap]
rs806610	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap]
rs809363	0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs9633155	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv995042	chrX:65121634-65953299	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv916393	chrX:65269672-65521616	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3350331	chrX:65287003-65495627	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:65383600-65442200	Weak transcription	Small Intestine	intestine
2	chrX:65384600-65435600	Weak transcription	Left Ventricle	heart
3	chrX:65385600-65435600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chrX:65387600-65435400	Weak transcription	Aorta	Aorta
5	chrX:65388200-65417200	Weak transcription	Colonic Mucosa	Colon
6	chrX:65393800-65419600	Weak transcription	Fetal Intestine Small	intestine
7	chrX:65393800-65428000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chrX:65396000-65428000	Weak transcription	Ovary	ovary
9	chrX:65400400-65430600	Weak transcription	Fetal Heart	heart
10	chrX:65402600-65415800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chrX:65406200-65422000	Weak transcription	Fetal Kidney	kidney
12	chrX:65406400-65416400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chrX:65407000-65448000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chrX:65407400-65415200	Strong transcription	K562	blood
15	chrX:65407600-65422400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chrX:65408000-65418400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chrX:65408200-65415000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chrX:65408200-65419600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chrX:65408200-65420000	Weak transcription	Brain Angular Gyrus	brain
20	chrX:65408200-65420200	Weak transcription	Brain Cingulate Gyrus	brain
21	chrX:65408400-65430800	Weak transcription	NH-A	brain
22	chrX:65408400-65436000	Weak transcription	Brain Substantia Nigra	brain
23	chrX:65408800-65420200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chrX:65409000-65415000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chrX:65409800-65422800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chrX:65411400-65415000	Strong transcription	Fetal Intestine Large	intestine
27	chrX:65411800-65432000	Weak transcription	Colon Smooth Muscle	Colon
28	chrX:65412000-65427400	Weak transcription	Fetal Lung	lung
29	chrX:65412200-65417600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chrX:65412200-65420200	Weak transcription	Rectal Smooth Muscle	rectum
31	chrX:65412400-65415000	Weak transcription	Stomach Smooth Muscle	stomach
32	chrX:65412400-65417400	Weak transcription	Fetal Stomach	stomach
33	chrX:65412600-65416000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
34	chrX:65412800-65416000	Weak transcription	Duodenum Mucosa	Duodenum
35	chrX:65412800-65427000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chrX:65412800-65431000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chrX:65413000-65419800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chrX:65413400-65414800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chrX:65413600-65415200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chrX:65414000-65415800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chrX:65414200-65415000	Enhancers	Dnd41	blood
42	chrX:65414200-65415400	Weak transcription	Esophagus	oesophagus
43	chrX:65414400-65414800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chrX:65414400-65435400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chrX:65414600-65415800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chrX:65414600-65417600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chrX:65414600-65417800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links