Variant report

Variant	rs12906566
Chromosome Location	chr15:57514874-57514875
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57514341..57517314-chr15:57518774..57520989,2	MCF-7	breast:
2	chr15:57506333..57510182-chr15:57512015..57516171,5	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1037956	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1037958	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10518899	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11071309	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11629653	0.85[EUR][1000 genomes]
rs11630910	0.85[EUR][1000 genomes]
rs11631084	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632069	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633061	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634352	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635440	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636201	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636340	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636348	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636919	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637955	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853331	0.80[EUR][1000 genomes]
rs11856055	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11856073	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11857507	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857722	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11858783	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11858880	0.87[EUR][1000 genomes]
rs12050751	0.94[EUR][1000 genomes]
rs12050758	0.94[EUR][1000 genomes]
rs12898356	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12899036	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899588	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12901671	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902099	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902170	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12902581	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903115	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903151	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903221	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903578	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12904189	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904321	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904501	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904561	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904602	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12904933	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906042	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906335	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908278	0.85[EUR][1000 genomes]
rs12908760	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909016	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910094	0.80[EUR][1000 genomes]
rs12910556	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12910832	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911256	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911297	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911518	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12912210	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912353	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912392	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912868	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12914425	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914481	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915473	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12915489	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12916478	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12917093	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1462156	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1545728	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17239431	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17239508	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1814585	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867641	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278685	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290938	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414491	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414492	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414494	0.81[EUR][1000 genomes]
rs2414497	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2431023	0.81[ASN][1000 genomes]
rs2441925	0.81[EUR][1000 genomes]
rs2593235	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593237	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2593238	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2615252	0.81[ASN][1000 genomes]
rs2703596	0.80[EUR][1000 genomes]
rs2733341	0.89[ASN][1000 genomes]
rs3794613	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238321	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4238322	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4303429	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4353440	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4369592	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4447362	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774250	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774251	0.85[EUR][1000 genomes]
rs4774252	0.85[EUR][1000 genomes]
rs4774913	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774918	0.85[EUR][1000 genomes]
rs4774919	0.85[EUR][1000 genomes]
rs5014892	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61996955	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62022237	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7161965	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs745652	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs898901	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935326	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs960946	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs978274	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12906566	TCF12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
3	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
5	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
6	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
7	chr15:57501200-57524400	Weak transcription	Thymus	Thymus
8	chr15:57507000-57519800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:57508200-57522800	Weak transcription	Fetal Thymus	thymus
10	chr15:57508600-57524400	Weak transcription	HepG2	liver
11	chr15:57508800-57515200	Weak transcription	K562	blood
12	chr15:57509200-57526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:57510600-57516400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:57510600-57517200	Active TSS	NHLF	lung
15	chr15:57510600-57518800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:57510600-57519400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:57510600-57519800	Weak transcription	Dnd41	blood
18	chr15:57510600-57524400	Weak transcription	Liver	Liver
19	chr15:57510600-57524600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr15:57511200-57525400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:57511400-57515000	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr15:57511400-57515200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:57511400-57515200	Weak transcription	Primary T cells from cord blood	blood
24	chr15:57511600-57525600	Weak transcription	A549	lung
25	chr15:57511600-57528000	Weak transcription	Fetal Heart	heart
26	chr15:57511800-57516200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:57511800-57516600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:57511800-57519400	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:57511800-57519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:57511800-57520600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:57511800-57520800	Weak transcription	Small Intestine	intestine
32	chr15:57511800-57524400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:57511800-57524400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:57511800-57524400	Weak transcription	HMEC	breast
35	chr15:57511800-57524600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr15:57511800-57524600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:57511800-57525800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:57511800-57528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:57512000-57515200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr15:57512000-57523400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:57512000-57524600	Weak transcription	Primary B cells from cord blood	blood
44	chr15:57512000-57527200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:57512200-57518600	Weak transcription	Brain Germinal Matrix	brain
46	chr15:57512200-57524400	Weak transcription	Left Ventricle	heart
47	chr15:57512200-57524600	Weak transcription	Ovary	ovary
48	chr15:57512600-57515000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:57512600-57524400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:57512600-57524400	Weak transcription	Fetal Intestine Large	intestine

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