Variant report

Variant	rs9302200
Chromosome Location	chr15:57331029-57331030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57285454..57287142-chr15:57328507..57331190,2	K562	blood:
2	chr15:57325288..57327004-chr15:57330879..57332478,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10467927	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs10467928	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs10467929	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs11071303	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11071308	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs11856411	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12324092	0.82[TSI][hapmap]
rs13379847	1.00[CEU][hapmap]
rs1430820	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs1430822	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs1441236	0.83[TSI][hapmap]
rs16977153	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs16977222	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16977243	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs16977270	0.85[CEU][hapmap]
rs16977278	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs17415731	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2169467	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs2414493	0.91[CEU][hapmap]
rs2593211	0.81[GIH][hapmap];0.89[TSI][hapmap]
rs2593252	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs2703614	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs2733333	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs28360967	0.87[EUR][1000 genomes]
rs28372003	0.81[EUR][1000 genomes]
rs28422021	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28505122	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28533433	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28541606	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28612876	0.87[EUR][1000 genomes]
rs28648577	0.87[EUR][1000 genomes]
rs28649108	0.87[EUR][1000 genomes]
rs28654848	0.87[EUR][1000 genomes]
rs28677775	0.84[EUR][1000 genomes]
rs28712697	0.81[EUR][1000 genomes]
rs28756149	0.84[EUR][1000 genomes]
rs28814080	0.82[EUR][1000 genomes]
rs4774245	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6493900	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs7162194	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs7163267	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs7164655	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7169053	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7171073	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7171304	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173748	0.90[CHB][hapmap]
rs7175191	0.87[TSI][hapmap]
rs7176873	0.92[CEU][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7178833	0.83[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs8023343	0.94[ASW][hapmap];0.85[CEU][hapmap];0.85[JPT][hapmap]
rs8023736	0.85[EUR][1000 genomes]
rs8023816	0.87[EUR][1000 genomes]
rs8026702	0.89[TSI][hapmap]
rs8031516	0.87[EUR][1000 genomes]
rs8031640	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8032615	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8033010	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8034066	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs8034744	0.83[TSI][hapmap]
rs8035485	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs8035916	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs8039899	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs8040708	0.85[EUR][1000 genomes]
rs9672676	0.83[TSI][hapmap]
rs9806170	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs9806199	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][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	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	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
4	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
5	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
rs9302200	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs9302200	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57309400-57334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
3	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:57318600-57335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:57324200-57331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:57324200-57331800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:57324200-57332600	Weak transcription	Fetal Lung	lung
8	chr15:57324200-57337800	Weak transcription	Psoas Muscle	Psoas
9	chr15:57324200-57339000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:57324200-57341200	Weak transcription	Fetal Stomach	stomach
11	chr15:57324400-57332600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:57324400-57338000	Weak transcription	HSMM	muscle
13	chr15:57324400-57341200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:57324600-57331400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
17	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:57324800-57347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
20	chr15:57325000-57334600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:57325400-57332600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:57326400-57341000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:57326600-57331200	Weak transcription	HepG2	liver
24	chr15:57326600-57331400	Weak transcription	Brain Angular Gyrus	brain
25	chr15:57326800-57332400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:57327200-57332600	Weak transcription	Liver	Liver
27	chr15:57327800-57332600	Enhancers	Brain Hippocampus Middle	brain
28	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
29	chr15:57328400-57332600	Weak transcription	Gastric	stomach
30	chr15:57328400-57333600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:57328400-57341200	Weak transcription	Ovary	ovary
32	chr15:57328400-57343800	Weak transcription	Small Intestine	intestine
33	chr15:57328400-57345800	Weak transcription	Left Ventricle	heart
34	chr15:57328600-57331200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:57328600-57355000	Weak transcription	Dnd41	blood
36	chr15:57328800-57331200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:57328800-57331400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:57328800-57331600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:57328800-57331600	Weak transcription	Brain Anterior Caudate	brain
40	chr15:57328800-57331800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:57328800-57332400	Weak transcription	Fetal Brain Male	brain
42	chr15:57328800-57332800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:57328800-57336400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:57329200-57331600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:57329200-57332600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:57329400-57331200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:57329400-57331400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:57329400-57331400	Weak transcription	Fetal Heart	heart
49	chr15:57329800-57331800	Weak transcription	HSMMtube	muscle
50	chr15:57329800-57334000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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