Variant report

Variant	rs534005
Chromosome Location	chr15:56985015-56985016
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1010699	0.90[EUR][1000 genomes]
rs11071282	0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs11071283	0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs11630334	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634444	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634704	0.85[ASN][1000 genomes]
rs11635201	0.97[ASN][1000 genomes]
rs11636534	0.90[EUR][1000 genomes]
rs12441674	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1657928	0.82[EUR][1000 genomes]
rs1657932	0.82[EUR][1000 genomes]
rs1657933	0.83[EUR][1000 genomes]
rs1657942	0.82[EUR][1000 genomes]
rs1660965	0.82[EUR][1000 genomes]
rs1680488	0.85[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16977060	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16977067	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2113678	0.90[EUR][1000 genomes]
rs2128172	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28441487	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28463927	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28497695	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28620046	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28678122	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs28778716	0.90[ASN][1000 genomes]
rs28830569	0.90[ASN][1000 genomes]
rs28893316	0.90[ASN][1000 genomes]
rs4774890	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774891	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7164084	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7182346	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72744954	0.90[ASN][1000 genomes]
rs72744977	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8031966	1.00[CEU][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809459	0.94[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
2	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:56917800-56990600	Weak transcription	NHLF	lung
4	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
5	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:56924000-56990800	Weak transcription	NHEK	skin
7	chr15:56928400-56996800	Weak transcription	Gastric	stomach
8	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
9	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
11	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
12	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:56946200-56990800	Weak transcription	Right Ventricle	heart
14	chr15:56955800-56990600	Weak transcription	Esophagus	oesophagus
15	chr15:56958000-56990200	Weak transcription	A549	lung
16	chr15:56958200-56990200	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:56958400-56990600	Weak transcription	Lung	lung
18	chr15:56958400-56990800	Weak transcription	Brain Germinal Matrix	brain
19	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
20	chr15:56958600-56990600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:56959200-56990400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:56959200-56990600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:56959200-56990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:56959200-56990600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:56959200-56992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:56959400-56986000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:56960800-56992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr15:56961200-56990600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:56961200-56992200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:56965600-56990800	Weak transcription	K562	blood
31	chr15:56967000-56990800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:56967600-56990600	Weak transcription	Left Ventricle	heart
33	chr15:56968400-56990600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:56968400-56992000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:56968400-56992000	Weak transcription	HSMMtube	muscle
36	chr15:56968600-56990000	Weak transcription	NH-A	brain
37	chr15:56968800-56990000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:56968800-56990200	Weak transcription	Osteobl	bone
39	chr15:56969000-56990800	Weak transcription	HMEC	breast
40	chr15:56969400-56990200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:56969400-56990400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr15:56969400-56990800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:56969600-56990200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:56969600-56990200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:56969800-56990200	Weak transcription	Primary B cells from cord blood	blood
46	chr15:56969800-56990600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:56969800-56990600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:56969800-56990600	Weak transcription	Brain Angular Gyrus	brain
49	chr15:56969800-56990800	Weak transcription	HepG2	liver
50	chr15:56970400-56988800	Weak transcription	Liver	Liver

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