Variant report

Variant	rs17236502
Chromosome Location	chr15:59558438-59558439
allele	G/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	CEBPB	chr15:59558265-59558610	H1-hESC	embryonic stem cell:	n/a	chr15:59558423-59558434 chr15:59558421-59558434
2	POLR2A	chr15:59557930-59558559	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr15:59558135-59558559	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOS	chr15:59558267-59558596	MCF10A-Er-Src	breast:	n/a	n/a
5	TEAD4	chr15:59558238-59558578	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:59558214-59558615	GM12892	blood:	n/a	n/a
7	FOS	chr15:59558315-59558531	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr15:59558174-59558852	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr15:59558271-59558452	GM12891	blood:	n/a	n/a
10	CEBPB	chr15:59558237-59558690	Hela-S3	cervix:	n/a	chr15:59558423-59558434 chr15:59558421-59558434
11	MYC	chr15:59558281-59558634	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr15:59558266-59558605	MCF10A-Er-Src	breast:	n/a	n/a
13	TEAD4	chr15:59558289-59558555	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr15:59558221-59558557	GM12891	blood:	n/a	n/a
15	FOS	chr15:59558229-59558604	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:59558248-59558498	Hela-S3	cervix:	n/a	n/a
17	TCF12	chr15:59558236-59558534	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF7L2	chr15:59558372-59559833	Hela-S3	cervix:	n/a	n/a
19	MYC	chr15:59558281-59558602	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr15:59558202-59558605	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr15:59558227-59558542	MCF10A-Er-Src	breast:	n/a	n/a
22	ELK4	chr15:59558333-59558886	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
MYO1E	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10775169	0.85[EUR][1000 genomes]
rs11855088	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437559	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437571	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439560	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441621	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12443328	0.94[CEU][hapmap]
rs12593382	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12595001	0.84[CEU][hapmap]
rs12595677	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912088	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12917076	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17236495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17236509	0.89[CEU][hapmap]
rs17302240	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17302247	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306783	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306784	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414624	0.81[EUR][1000 genomes]
rs28368974	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34310505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34540528	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34827755	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794489	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4074433	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4074434	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4077169	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4287498	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4420472	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4482215	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4597251	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4775137	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56752228	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494091	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67037466	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67599725	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68078916	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68084852	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166002	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7180541	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72625730	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72746841	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8030006	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8031729	0.89[CEU][hapmap]
rs8039095	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
2	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
4	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:59524600-59574600	Weak transcription	Lung	lung
6	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
7	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:59530600-59568000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:59530800-59569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:59533400-59559800	Weak transcription	NHLF	lung
11	chr15:59533400-59564000	Weak transcription	Ovary	ovary
12	chr15:59533400-59566800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:59536600-59559000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:59540000-59560000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:59540000-59568800	Weak transcription	Fetal Kidney	kidney
16	chr15:59540600-59561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:59541200-59566400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:59542400-59568200	Weak transcription	Gastric	stomach
19	chr15:59542600-59559800	Weak transcription	Spleen	Spleen
20	chr15:59542600-59563000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:59542800-59565400	Weak transcription	Left Ventricle	heart
22	chr15:59543200-59568200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:59544000-59566200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:59544600-59582400	Weak transcription	Primary B cells from cord blood	blood
25	chr15:59545000-59560000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:59547400-59559600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:59547400-59564000	Weak transcription	Fetal Stomach	stomach
28	chr15:59547400-59587000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:59548200-59559600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:59548200-59560600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:59548200-59566400	Weak transcription	Aorta	Aorta
32	chr15:59548200-59567800	Weak transcription	Fetal Heart	heart
33	chr15:59548600-59560000	Weak transcription	NH-A	brain
34	chr15:59549800-59559800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:59550000-59558600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:59550000-59561400	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:59550000-59568000	Weak transcription	Colonic Mucosa	Colon
38	chr15:59550000-59571600	Weak transcription	Esophagus	oesophagus
39	chr15:59550200-59566000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:59550600-59574600	Weak transcription	Adipose Nuclei	Adipose
41	chr15:59551400-59566200	Weak transcription	HSMMtube	muscle
42	chr15:59552000-59569800	Weak transcription	Brain Anterior Caudate	brain
43	chr15:59552200-59559800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:59552600-59560000	Weak transcription	HUVEC	blood vessel
45	chr15:59552600-59564000	Strong transcription	GM12878-XiMat	blood
46	chr15:59552600-59566400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:59552800-59559600	Weak transcription	Osteobl	bone
48	chr15:59553200-59559600	Weak transcription	Brain Angular Gyrus	brain
49	chr15:59553200-59560200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:59553400-59560400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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