Variant report

Variant	rs28417201
Chromosome Location	chrX:79956549-79956550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11796018	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[TSI][hapmap];1.00[YRI][hapmap]
rs12689192	0.80[CHD][hapmap]
rs16979508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs16979519	0.80[CHD][hapmap]
rs3106407	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3122406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3123257	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3132154	0.94[CEU][hapmap]
rs3923574	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4240018	0.94[CEU][hapmap]
rs4567187	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4826192	0.90[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[TSI][hapmap];0.95[YRI][hapmap]
rs5912437	0.88[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap]
rs7049509	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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7059257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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	nsv916218	chrX:79377399-80230929	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv532882	chrX:79884715-80017999	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv524776	chrX:79903169-80012807	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv533969	chrX:79915477-79989648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:79926200-79978000	Weak transcription	NH-A	brain
2	chrX:79928600-79962000	Weak transcription	Fetal Brain Female	brain
3	chrX:79930600-79959800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chrX:79930800-79962400	Weak transcription	Right Ventricle	heart
5	chrX:79930800-79987600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chrX:79931000-79971000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chrX:79931000-79982800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chrX:79931200-79960600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chrX:79931200-79985600	Weak transcription	A549	lung
10	chrX:79932800-79964200	Weak transcription	Colon Smooth Muscle	Colon
11	chrX:79932800-79984800	Weak transcription	Brain Anterior Caudate	brain
12	chrX:79933000-79961000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chrX:79933000-79972200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chrX:79933400-79972000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chrX:79933400-79984600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chrX:79934600-79975200	Weak transcription	GM12878-XiMat	blood
17	chrX:79934800-79961600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chrX:79935400-79986800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chrX:79936000-79977600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chrX:79936200-79980800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chrX:79936600-80000200	Weak transcription	Small Intestine	intestine
22	chrX:79937000-79982000	Weak transcription	HSMMtube	muscle
23	chrX:79937000-80003600	Weak transcription	Fetal Lung	lung
24	chrX:79938400-79956800	Weak transcription	Brain Substantia Nigra	brain
25	chrX:79938400-79959000	Weak transcription	HUVEC	blood vessel
26	chrX:79940200-79972600	Weak transcription	Fetal Kidney	kidney
27	chrX:79940400-79964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chrX:79942600-79977600	Weak transcription	HSMM	muscle
29	chrX:79943800-79984800	Weak transcription	Brain Germinal Matrix	brain
30	chrX:79944000-79969800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chrX:79947200-79975400	Weak transcription	Pancreas	Pancrea
32	chrX:79950200-79971400	Weak transcription	Spleen	Spleen
33	chrX:79950200-79980000	Weak transcription	Esophagus	oesophagus
34	chrX:79950400-79959200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chrX:79950400-79959400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chrX:79950400-79971600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chrX:79950400-80001600	Weak transcription	Placenta	Placenta
38	chrX:79950600-79957000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chrX:79950600-79963200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chrX:79950600-79965400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chrX:79950600-79968400	Weak transcription	Aorta	Aorta
42	chrX:79950600-79978800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chrX:79950600-80012000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chrX:79950800-79958800	Weak transcription	Liver	Liver
45	chrX:79950800-79962200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chrX:79950800-79964800	Weak transcription	Left Ventricle	heart
47	chrX:79950800-79974600	Weak transcription	Gastric	stomach
48	chrX:79950800-79977200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chrX:79950800-79977800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chrX:79950800-79978000	Weak transcription	Fetal Muscle Trunk	muscle

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