Variant report

Variant	rs9990771
Chromosome Location	chr4:54132720-54132721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10014030	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10027975	0.81[AFR][1000 genomes]
rs11133257	0.83[CEU][hapmap]
rs11133258	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11721940	0.96[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11724062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11724781	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11725172	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11942132	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12715997	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13130337	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1383981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1383983	0.83[CEU][hapmap]
rs1481818	0.85[CEU][hapmap]
rs1842658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871826	0.85[CEU][hapmap]
rs2200051	0.80[EUR][1000 genomes]
rs2412403	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2412404	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs28832663	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34426398	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4328970	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4472196	0.83[CEU][hapmap]
rs4571396	0.82[CEU][hapmap]
rs4588514	0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs4864742	0.81[EUR][1000 genomes]
rs4864749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62324286	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6554071	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6554074	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6554078	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6554089	0.83[CEU][hapmap]
rs6554091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554092	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6554093	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6821113	0.84[EUR][1000 genomes]
rs6852852	0.83[EUR][1000 genomes]
rs6856562	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6857744	0.81[EUR][1000 genomes]
rs751266	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7655632	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7657388	0.83[CEU][hapmap]
rs7658384	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7673864	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7682970	0.85[CEU][hapmap]
rs7683984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs900110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs922748	0.83[CEU][hapmap]
rs9759746	0.83[EUR][1000 genomes]
rs9991945	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9998376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv997614	chr4:54086727-54150632	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879013	chr4:54093717-54137228	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2763360	chr4:54123894-54153814	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54114400-54134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:54114400-54139600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:54114400-54144000	Weak transcription	Liver	Liver
4	chr4:54117800-54132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:54122200-54139800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:54126600-54134200	Weak transcription	Gastric	stomach
7	chr4:54126800-54141400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54127600-54153000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:54128000-54134400	Weak transcription	Pancreas	Pancrea
10	chr4:54128200-54136200	Weak transcription	Thymus	Thymus
11	chr4:54128600-54132800	Weak transcription	Adipose Nuclei	Adipose
12	chr4:54129600-54141400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:54129600-54154600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:54129800-54145200	Weak transcription	Fetal Lung	lung
15	chr4:54130000-54134600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:54130000-54135800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:54130200-54134400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:54130400-54134200	Weak transcription	Spleen	Spleen
19	chr4:54130400-54134400	Weak transcription	Primary T cells from cord blood	blood
20	chr4:54130400-54143400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:54130400-54148600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:54130400-54150400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:54130600-54133800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:54130600-54134200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:54130600-54134200	Weak transcription	Fetal Stomach	stomach
26	chr4:54130600-54134400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr4:54130600-54134600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:54130600-54135000	Weak transcription	Fetal Intestine Large	intestine
29	chr4:54130600-54136000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:54130600-54137200	Weak transcription	Esophagus	oesophagus
31	chr4:54130600-54148200	Weak transcription	Fetal Intestine Small	intestine
32	chr4:54130800-54134200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:54130800-54134200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:54130800-54134200	Weak transcription	NHLF	lung
35	chr4:54130800-54134600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:54130800-54134800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:54131000-54145800	Weak transcription	Primary B cells from cord blood	blood
38	chr4:54131200-54133800	Weak transcription	NHDF-Ad	bronchial
39	chr4:54131800-54133600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:54132400-54135800	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:54132600-54134200	Weak transcription	Left Ventricle	heart
42	chr4:54132600-54134200	Weak transcription	Stomach Smooth Muscle	stomach

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