Variant report

Variant	rs12904501
Chromosome Location	chr15:57507617-57507618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr15:57507509-57507752	HepG2	liver:	n/a	n/a
2	STAT3	chr15:57507517-57507847	MCF10A-Er-Src	breast:	n/a	n/a
3	FAM48A	chr15:57507533-57507654	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:57210007..57212139-chr15:57506855..57509389,2	K562	blood:
2	chr15:57507579..57509152-chr15:57511369..57513515,2	K562	blood:
3	chr15:57506333..57510182-chr15:57512015..57516171,5	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region
ENSG00000137871	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1037956	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1037958	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10518899	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11071309	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11629653	0.82[EUR][1000 genomes]
rs11630910	0.82[EUR][1000 genomes]
rs11631084	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632069	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633061	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634352	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11635440	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636201	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636340	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636348	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636919	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637955	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11853331	0.84[EUR][1000 genomes]
rs11856055	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11856073	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11857507	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857722	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11858783	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11858880	0.91[EUR][1000 genomes]
rs12050751	0.98[EUR][1000 genomes]
rs12050758	0.98[EUR][1000 genomes]
rs12898356	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12899036	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899588	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12901671	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902099	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902170	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12902581	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903115	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903151	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903221	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903578	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12904189	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904561	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904602	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12904933	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906042	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906335	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906566	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908278	0.82[EUR][1000 genomes]
rs12908760	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909016	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12910094	0.84[EUR][1000 genomes]
rs12910556	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12910832	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911256	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911297	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911518	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12912210	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912353	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912392	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12912868	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12914182	0.81[EUR][1000 genomes]
rs12914410	0.82[EUR][1000 genomes]
rs12914425	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914481	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915473	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12915489	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12916478	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12917093	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1462156	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1545728	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17239431	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17239508	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1814585	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867641	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278685	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290938	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414491	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414492	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414494	0.85[EUR][1000 genomes]
rs2414497	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2431023	0.81[ASN][1000 genomes]
rs2593235	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593237	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2593238	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2615252	0.81[ASN][1000 genomes]
rs2703596	0.83[EUR][1000 genomes]
rs2733341	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794613	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4238321	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4238322	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4303429	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4353440	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4369592	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4447362	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774250	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774251	0.82[EUR][1000 genomes]
rs4774252	0.82[EUR][1000 genomes]
rs4774913	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774918	0.82[EUR][1000 genomes]
rs4774919	0.82[EUR][1000 genomes]
rs5014892	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61996955	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62022237	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7161965	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs745652	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs898901	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935326	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs960946	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs978274	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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
rs12904501	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 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	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:57491400-57510000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:57491400-57510000	Weak transcription	Psoas Muscle	Psoas
11	chr15:57491400-57510200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:57491400-57511200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:57491600-57508000	Weak transcription	HUVEC	blood vessel
14	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
15	chr15:57492400-57511600	Weak transcription	Left Ventricle	heart
16	chr15:57494200-57508600	Weak transcription	Dnd41	blood
17	chr15:57496400-57508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:57496400-57510200	Weak transcription	Small Intestine	intestine
19	chr15:57501200-57524400	Weak transcription	Thymus	Thymus
20	chr15:57501600-57510200	Weak transcription	Primary B cells from cord blood	blood
21	chr15:57502400-57509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:57503000-57510400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:57503400-57508600	Weak transcription	Primary T cells from cord blood	blood
24	chr15:57504200-57508200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:57504400-57510200	Enhancers	Brain Hippocampus Middle	brain
26	chr15:57504600-57510000	Enhancers	Brain Anterior Caudate	brain
27	chr15:57504800-57510200	Enhancers	Brain Substantia Nigra	brain
28	chr15:57505000-57509800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:57505000-57510000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:57505000-57510200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:57505200-57508000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:57505200-57508000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:57505200-57508200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:57505200-57508200	Enhancers	NHLF	lung
35	chr15:57505200-57510000	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:57505200-57511400	Enhancers	Fetal Lung	lung
37	chr15:57505400-57508400	Enhancers	HSMM	muscle
38	chr15:57505800-57507800	Enhancers	HepG2	liver
39	chr15:57505800-57508200	Enhancers	Osteobl	bone
40	chr15:57505800-57509800	Enhancers	NHDF-Ad	bronchial
41	chr15:57505800-57510000	Enhancers	Fetal Kidney	kidney
42	chr15:57506000-57509200	Enhancers	A549	lung
43	chr15:57506000-57511600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:57506200-57508200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:57506200-57508200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:57506200-57508600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:57506400-57508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:57506400-57508200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr15:57506400-57508400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:57506400-57510000	Weak transcription	Primary monocytes fromperipheralblood	blood

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