Variant report

Variant	rs12442189
Chromosome Location	chr15:56952093-56952094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10152127	0.81[ASN][1000 genomes]
rs10518870	0.88[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs11071280	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630168	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11633363	0.86[EUR][1000 genomes]
rs11635333	0.87[EUR][1000 genomes]
rs11636994	0.80[ASN][1000 genomes]
rs11638707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11852277	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856558	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11857388	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11857706	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12148500	0.84[ASN][1000 genomes]
rs12591502	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592389	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12898521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12898760	0.87[EUR][1000 genomes]
rs12900244	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12901887	0.82[CEU][hapmap]
rs12903283	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903336	0.92[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12903862	0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12905514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12906830	0.84[EUR][1000 genomes]
rs12908906	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12910442	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12910459	0.89[CEU][hapmap]
rs12911191	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12911381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12912666	0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs12913361	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12916079	0.93[EUR][1000 genomes]
rs1424694	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs16977020	0.95[CHB][hapmap]
rs17238845	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979467	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1994081	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2170459	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2170463	0.88[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2279298	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2279299	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs2414480	0.87[EUR][1000 genomes]
rs28480089	0.85[EUR][1000 genomes]
rs28620278	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784554	0.84[EUR][1000 genomes]
rs3803457	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3816752	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs3929265	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4774244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs4774884	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774886	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs538382	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs553421	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7162317	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7168178	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs7174432	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7178796	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182187	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs795032	0.81[EUR][1000 genomes]
rs8025391	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs8036217	0.87[EUR][1000 genomes]
rs8041540	0.87[EUR][1000 genomes]
rs8043223	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1041239	chr15:56888945-56959028	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island 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	chr15:56912800-56957000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr15:56913400-56955200	Weak transcription	Aorta	Aorta
3	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
4	chr15:56917200-56955200	Weak transcription	Psoas Muscle	Psoas
5	chr15:56917600-56957000	Weak transcription	Brain Anterior Caudate	brain
6	chr15:56917800-56955800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:56917800-56956800	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:56917800-56959800	Weak transcription	Brain Angular Gyrus	brain
9	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:56917800-56990600	Weak transcription	NHLF	lung
11	chr15:56918400-56957200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:56919600-56955200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
14	chr15:56920000-56953000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:56921600-56955200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:56921600-56955400	Weak transcription	NH-A	brain
17	chr15:56922000-56954800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:56922000-56958000	Weak transcription	Lung	lung
19	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:56924000-56990800	Weak transcription	NHEK	skin
21	chr15:56924200-56955400	Weak transcription	Fetal Brain Female	brain
22	chr15:56924600-56957200	Weak transcription	HUVEC	blood vessel
23	chr15:56928400-56996800	Weak transcription	Gastric	stomach
24	chr15:56930000-56954800	Weak transcription	Fetal Stomach	stomach
25	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
26	chr15:56938600-56968200	Weak transcription	HMEC	breast
27	chr15:56939200-56953800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:56939400-56955600	Weak transcription	Fetal Heart	heart
30	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
31	chr15:56941400-56960200	Weak transcription	Spleen	Spleen
32	chr15:56943600-56955600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:56943600-56958000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:56944200-56959600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:56944400-56954800	Weak transcription	Esophagus	oesophagus
36	chr15:56944400-56957600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:56944600-56964600	Weak transcription	K562	blood
38	chr15:56944800-56960800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:56944800-56962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:56945200-56963200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:56945800-56953200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:56945800-56955600	Weak transcription	A549	lung
43	chr15:56945800-56963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
45	chr15:56946000-56955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:56946000-56957800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:56946200-56954000	Weak transcription	Placenta	Placenta
49	chr15:56946200-56954800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:56946200-56955000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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