Variant report

Variant	rs7162194
Chromosome Location	chr15:57281391-57281392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57212275..57213860-chr15:57281190..57283282,2	K562	blood:
2	chr15:57254284..57256820-chr15:57279086..57281932,2	K562	blood:
3	chr15:57277206..57280483-chr15:57280538..57284418,3	K562	blood:
4	chr15:57275197..57277151-chr15:57278136..57281602,3	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs10467928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10467929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10851612	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11071303	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11071308	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1115019	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11856411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901355	0.85[EUR][1000 genomes]
rs13379847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs1430820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1441236	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1657922	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs16977153	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16977222	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs16977270	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs16977278	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17415731	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1820994	0.85[ASN][1000 genomes]
rs2169467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2278613	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2464429	0.89[YRI][hapmap]
rs2464430	0.89[YRI][hapmap]
rs2470079	0.89[YRI][hapmap]
rs2470082	0.88[YRI][hapmap]
rs2593211	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2593249	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2593252	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2703576	0.93[YRI][hapmap]
rs2703614	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2733188	0.93[YRI][hapmap]
rs2733332	0.81[YRI][hapmap]
rs2733333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2733334	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs28360967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28422021	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28505122	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28533433	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28541606	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28612876	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28649108	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28654848	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28677775	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28756149	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28814080	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28856894	0.89[EUR][1000 genomes]
rs2920267	0.92[YRI][hapmap]
rs2951899	0.91[YRI][hapmap]
rs2951903	0.93[YRI][hapmap]
rs2951904	0.92[YRI][hapmap]
rs2962991	0.89[YRI][hapmap]
rs2962992	0.85[YRI][hapmap]
rs4774245	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6493900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6493902	0.92[YRI][hapmap]
rs7163267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs7164655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169053	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7171073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7173748	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs7175191	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7175436	0.88[YRI][hapmap]
rs7176873	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178833	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023343	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs8023816	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8031516	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033010	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034502	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs8035485	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs8035916	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs8039899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040708	0.95[EUR][1000 genomes]
rs9302200	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs9806170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap]
rs9806199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7162194	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7162194	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57272200-57282400	Enhancers	Primary T cells from cord blood	blood
3	chr15:57273000-57281400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:57273000-57281600	Weak transcription	Ovary	ovary
5	chr15:57273000-57283200	Weak transcription	Spleen	Spleen
6	chr15:57273000-57285800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
8	chr15:57273600-57281600	Weak transcription	K562	blood
9	chr15:57274000-57287600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:57274200-57289200	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:57274200-57295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:57276200-57282600	Enhancers	Brain Substantia Nigra	brain
14	chr15:57276200-57284000	Weak transcription	Lung	lung
15	chr15:57276200-57289200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr15:57276600-57282000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:57276600-57282200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr15:57276600-57283000	Weak transcription	Left Ventricle	heart
20	chr15:57276600-57283200	Weak transcription	Right Atrium	heart
21	chr15:57276600-57288000	Weak transcription	Aorta	Aorta
22	chr15:57276800-57288600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:57277000-57281400	Enhancers	A549	lung
24	chr15:57277000-57281800	Weak transcription	Thymus	Thymus
25	chr15:57277000-57285400	Weak transcription	Fetal Intestine Large	intestine
26	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:57277400-57281400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57277600-57281800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:57277600-57287600	Weak transcription	Brain Germinal Matrix	brain
30	chr15:57277800-57281400	Weak transcription	Adipose Nuclei	Adipose
31	chr15:57277800-57281400	Weak transcription	Hela-S3	cervix
32	chr15:57277800-57281600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:57277800-57281800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:57277800-57285000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:57278000-57281600	Weak transcription	HMEC	breast
36	chr15:57278000-57281600	Weak transcription	NHLF	lung
37	chr15:57278000-57282800	Enhancers	Brain Hippocampus Middle	brain
38	chr15:57278000-57285400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:57278200-57281400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:57278200-57281600	Weak transcription	Primary B cells from cord blood	blood
41	chr15:57278200-57282200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:57278200-57282200	Enhancers	NHDF-Ad	bronchial
43	chr15:57278200-57282200	Enhancers	Osteobl	bone
44	chr15:57278400-57281600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr15:57278400-57281600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:57278600-57281600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:57278600-57282000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:57278600-57295400	Weak transcription	NH-A	brain
49	chr15:57279000-57281400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:57279000-57281600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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