Variant report

Variant	rs12592389
Chromosome Location	chr15:56960626-56960627
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	chr15:56947710..56949371-chr15:56958566..56961070,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10152127	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518870	0.84[CEU][hapmap]
rs11071280	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630168	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633363	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635333	0.85[EUR][1000 genomes]
rs11636994	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11638707	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11852277	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856558	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857388	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857706	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148500	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438709	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12442018	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442189	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]
rs12591502	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593286	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12898521	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12898760	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900244	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12903283	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903336	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903862	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12905514	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap]
rs12906830	0.82[EUR][1000 genomes]
rs12908906	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910442	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12910459	0.85[CEU][hapmap]
rs12911191	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12911381	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912666	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[TSI][hapmap]
rs12913361	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12916079	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1424694	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs16977020	0.86[CHB][hapmap]
rs17238845	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979467	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1994081	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052640	0.80[EUR][1000 genomes]
rs2170459	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170463	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279298	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279299	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2414480	0.85[EUR][1000 genomes]
rs28480089	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28620278	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784554	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3803457	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816752	0.84[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3929265	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774244	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs4774884	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774886	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs538382	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs553421	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs559736	0.85[EUR][1000 genomes]
rs7162317	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7165831	0.86[EUR][1000 genomes]
rs7168178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7169454	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7174432	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7178796	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182187	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8025391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8036217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8041540	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8043223	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]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12592389	TCF12	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56916600-56990800	Weak transcription	Pancreas	Pancrea
2	chr15:56917800-56990600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:56917800-56990600	Weak transcription	NHLF	lung
4	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
5	chr15:56924000-56990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:56924000-56990800	Weak transcription	NHEK	skin
7	chr15:56928400-56996800	Weak transcription	Gastric	stomach
8	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
9	chr15:56938600-56968200	Weak transcription	HMEC	breast
10	chr15:56939200-56990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:56939400-56986000	Weak transcription	Brain Substantia Nigra	brain
12	chr15:56944600-56964600	Weak transcription	K562	blood
13	chr15:56944800-56960800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:56944800-56962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:56945200-56963200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:56945800-56963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:56945800-56990800	Weak transcription	Fetal Brain Male	brain
18	chr15:56946000-56990800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:56946200-56971000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:56946200-56990800	Weak transcription	Right Ventricle	heart
21	chr15:56948200-56961400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:56950200-56969200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:56950400-56965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:56950600-56967200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:56951800-56960800	Strong transcription	Adipose Nuclei	Adipose
26	chr15:56952400-56960800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:56952800-56960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:56953000-56960800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:56953200-56961600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:56954000-56968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:56954200-56965200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:56954800-56969400	Strong transcription	Fetal Thymus	thymus
33	chr15:56955000-56960800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:56955000-56961200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:56955000-56961400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:56955200-56961200	Strong transcription	Primary T cells from cord blood	blood
37	chr15:56955200-56961200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr15:56955200-56962200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:56955800-56970200	Weak transcription	Psoas Muscle	Psoas
40	chr15:56955800-56990600	Weak transcription	Esophagus	oesophagus
41	chr15:56956000-56973400	Weak transcription	Aorta	Aorta
42	chr15:56957000-56960800	Strong transcription	HSMM	muscle
43	chr15:56957000-56961200	Strong transcription	Brain Anterior Caudate	brain
44	chr15:56957000-56961400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:56957400-56967800	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:56957400-56968000	Weak transcription	Fetal Heart	heart
47	chr15:56957400-56969000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:56957400-56969200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:56957400-56975600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:56958000-56990200	Weak transcription	A549	lung

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