Variant report

Variant	rs8043223
Chromosome Location	chr15:56953740-56953741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56946938..56949698-chr15:56952748..56954656,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10152127	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518870	0.84[CEU][hapmap]
rs11071280	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630168	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11633363	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635333	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11636994	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11638580	0.81[ASN][1000 genomes]
rs11638707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11852277	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856558	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857388	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11857706	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12148500	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12438709	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442018	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442189	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]
rs12591502	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593286	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12898521	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12898760	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900244	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12903283	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903336	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903862	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12905514	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs12906830	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908906	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910442	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910459	0.85[CEU][hapmap]
rs12911191	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911381	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912666	0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[TSI][hapmap]
rs12913361	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12916079	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1424694	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16977020	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs17238845	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979467	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1994081	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2170459	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170463	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279298	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279299	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2414480	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28480089	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28620278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784554	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803457	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816752	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs3929265	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774244	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4774884	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774886	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs521904	0.81[ASN][1000 genomes]
rs538382	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs553421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs559736	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7162317	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7165831	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7168178	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7169454	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7174432	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7178796	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182187	0.89[ASN][1000 genomes]
rs8025391	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8036217	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8041540	0.83[EUR][1000 genomes];0.84[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8043223	TCF12	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr15:56921600-56955200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:56921600-56955400	Weak transcription	NH-A	brain
16	chr15:56922000-56954800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:56922000-56958000	Weak transcription	Lung	lung
18	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:56924000-56990800	Weak transcription	NHEK	skin
20	chr15:56924200-56955400	Weak transcription	Fetal Brain Female	brain
21	chr15:56924600-56957200	Weak transcription	HUVEC	blood vessel
22	chr15:56928400-56996800	Weak transcription	Gastric	stomach
23	chr15:56930000-56954800	Weak transcription	Fetal Stomach	stomach
24	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
25	chr15:56938600-56968200	Weak transcription	HMEC	breast
26	chr15:56939200-56953800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:56939400-56955600	Weak transcription	Fetal Heart	heart
29	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
30	chr15:56941400-56960200	Weak transcription	Spleen	Spleen
31	chr15:56943600-56955600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:56943600-56958000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:56944200-56959600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:56944400-56954800	Weak transcription	Esophagus	oesophagus
35	chr15:56944400-56957600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:56944600-56964600	Weak transcription	K562	blood
37	chr15:56944800-56960800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:56944800-56962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:56945200-56963200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:56945800-56955600	Weak transcription	A549	lung
41	chr15:56945800-56963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
43	chr15:56946000-56955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:56946000-56957800	Weak transcription	Fetal Intestine Small	intestine
45	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr15:56946200-56954000	Weak transcription	Placenta	Placenta
47	chr15:56946200-56954800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:56946200-56955000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:56946200-56955000	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:56946200-56955200	Weak transcription	Left Ventricle	heart

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