Variant report

Variant	rs12910556
Chromosome Location	chr15:57493210-57493211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57489288..57492189-chr15:57492368..57494008,2	MCF-7	breast:
2	chr15:57491334..57495003-chr15:57497716..57500211,4	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1037956	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1037958	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10518899	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071309	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11631084	0.81[EUR][1000 genomes]
rs11632069	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11633061	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11636201	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11636340	0.81[EUR][1000 genomes]
rs11636348	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11636919	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11637955	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11853331	0.82[EUR][1000 genomes]
rs11856055	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856073	0.81[EUR][1000 genomes]
rs11857507	0.82[EUR][1000 genomes]
rs11857722	0.81[EUR][1000 genomes]
rs11858783	0.92[EUR][1000 genomes]
rs11858880	0.89[EUR][1000 genomes]
rs12050751	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050758	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12898356	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899036	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12899588	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12901671	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12902099	0.81[EUR][1000 genomes]
rs12902170	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12903115	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12903151	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12903221	0.80[EUR][1000 genomes]
rs12903578	0.85[EUR][1000 genomes]
rs12904189	0.81[EUR][1000 genomes]
rs12904321	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904501	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904561	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12904602	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904933	0.82[EUR][1000 genomes]
rs12906042	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12906335	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12906566	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12908760	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12909016	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12910094	0.82[EUR][1000 genomes]
rs12910832	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911256	0.81[EUR][1000 genomes]
rs12911518	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912210	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912353	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12912392	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12912868	0.82[EUR][1000 genomes]
rs12914410	0.80[EUR][1000 genomes]
rs12914425	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12914481	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12915473	0.85[EUR][1000 genomes]
rs12915489	0.81[EUR][1000 genomes]
rs12916478	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12917093	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1462156	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1545728	0.81[EUR][1000 genomes]
rs17239431	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17239508	0.81[EUR][1000 genomes]
rs1814585	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1867641	0.91[EUR][1000 genomes]
rs2278685	0.81[EUR][1000 genomes]
rs2290938	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2414491	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414492	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414494	0.83[EUR][1000 genomes]
rs2414497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593237	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2593238	0.96[EUR][1000 genomes]
rs2703596	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733341	0.84[EUR][1000 genomes]
rs3794613	0.81[EUR][1000 genomes]
rs4303429	0.81[EUR][1000 genomes]
rs4353440	0.81[EUR][1000 genomes]
rs4369592	0.81[EUR][1000 genomes]
rs4447362	0.81[EUR][1000 genomes]
rs4774250	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4774913	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5014892	0.81[EUR][1000 genomes]
rs62022237	0.87[EUR][1000 genomes]
rs7161965	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs745652	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8033118	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898901	0.84[EUR][1000 genomes]
rs935326	0.81[EUR][1000 genomes]
rs978274	0.83[AMR][1000 genomes];0.91[EUR][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	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12910556	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57444400-57507400	Weak transcription	K562	blood
2	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:57457200-57499400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
5	chr15:57478600-57494000	Weak transcription	Pancreas	Pancrea
6	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
7	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
9	chr15:57483000-57493800	Weak transcription	Colonic Mucosa	Colon
10	chr15:57484800-57496200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:57484800-57502000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr15:57485000-57501000	Weak transcription	Spleen	Spleen
13	chr15:57485000-57501800	Weak transcription	Lung	lung
14	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:57485800-57493600	Weak transcription	A549	lung
17	chr15:57486600-57493400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:57486600-57496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
20	chr15:57487000-57496600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
22	chr15:57487200-57503000	Weak transcription	Liver	Liver
23	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:57488400-57494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:57488400-57496000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr15:57488400-57496000	Weak transcription	Fetal Intestine Small	intestine
28	chr15:57489200-57496000	Weak transcription	Osteobl	bone
29	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:57489800-57493400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr15:57489800-57494200	Strong transcription	Dnd41	blood
33	chr15:57490200-57494400	Enhancers	Brain Hippocampus Middle	brain
34	chr15:57490600-57505800	Weak transcription	NH-A	brain
35	chr15:57490800-57496400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:57491000-57493800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:57491000-57495000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:57491000-57501400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:57491000-57505600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:57491000-57506000	Weak transcription	HMEC	breast
41	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:57491400-57493600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr15:57491400-57493600	Weak transcription	Stomach Mucosa	stomach
44	chr15:57491400-57494200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:57491400-57496000	Weak transcription	Ovary	ovary
46	chr15:57491400-57497200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:57491400-57497200	Weak transcription	Right Atrium	heart
48	chr15:57491400-57497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:57491400-57500800	Weak transcription	Thymus	Thymus
50	chr15:57491400-57501200	Weak transcription	Primary B cells from cord blood	blood

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