Variant report

Variant	rs17082557
Chromosome Location	chr4:54140416-54140417
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10014172	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs10021659	0.84[YRI][hapmap]
rs10022429	0.84[YRI][hapmap]
rs10024153	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs10025091	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs10517295	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs12644212	0.84[ASW][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.84[YRI][hapmap]
rs12645287	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs1481816	0.92[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs1481822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs15834	0.83[YRI][hapmap]
rs17082492	1.00[ASW][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs17326196	0.84[YRI][hapmap]
rs17839071	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs1962230	1.00[ASW][hapmap];0.84[GIH][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2048709	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs2412487	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs28408605	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28496991	0.84[ASN][1000 genomes]
rs28524754	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28575132	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs28658460	0.96[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs28676739	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28704944	0.81[AFR][1000 genomes]
rs28826682	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28829603	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs28865315	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28874576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28887768	0.80[AFR][1000 genomes]
rs4555709	1.00[YRI][hapmap]
rs55744909	0.81[AFR][1000 genomes]
rs58424801	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62324293	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62325041	0.80[AFR][1000 genomes]
rs6810475	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811200	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6835821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73816160	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7680607	0.81[AFR][1000 genomes]
rs9312637	1.00[YRI][hapmap]
rs9884671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992110	1.00[ASW][hapmap];0.94[GIH][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs9994573	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9995661	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9997095	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	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	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
3	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54114400-54144000	Weak transcription	Liver	Liver
2	chr4:54126800-54141400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:54127600-54153000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:54129600-54141400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:54129600-54154600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:54129800-54145200	Weak transcription	Fetal Lung	lung
7	chr4:54130400-54143400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:54130400-54148600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:54130400-54150400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:54130600-54148200	Weak transcription	Fetal Intestine Small	intestine
11	chr4:54131000-54145800	Weak transcription	Primary B cells from cord blood	blood
12	chr4:54133000-54141400	Weak transcription	Placenta	Placenta
13	chr4:54133200-54144600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:54134800-54151000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:54134800-54154200	Weak transcription	NHLF	lung
16	chr4:54135000-54145600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:54135000-54145800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:54135000-54151200	Weak transcription	Left Ventricle	heart
19	chr4:54135200-54140800	Weak transcription	Pancreas	Pancrea
20	chr4:54135200-54142600	Weak transcription	GM12878-XiMat	blood
21	chr4:54135200-54144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:54135200-54148200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:54135200-54151800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:54135200-54154600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:54135400-54146000	Weak transcription	Fetal Stomach	stomach
26	chr4:54135400-54152200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:54135400-54153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:54139600-54140800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:54139600-54140800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:54140200-54143600	Weak transcription	HSMM	muscle
31	chr4:54140200-54151000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:54140200-54179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:54140400-54147200	Weak transcription	Osteobl	bone
34	chr4:54140400-54147600	Weak transcription	NHDF-Ad	bronchial

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