Variant report

Variant	rs12443328
Chromosome Location	chr15:59561741-59561742
allele	A/G
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	SP1	chr15:59560499-59561813	A549	lung:	n/a	n/a
2	CBX3	chr15:59561108-59561807	HCT-116	colon:	n/a	n/a
3	FOXA2	chr15:59560995-59561761	A549	lung:	n/a	n/a
4	TCF12	chr15:59560753-59562345	A549	lung:	n/a	n/a
5	MAX	chr15:59560874-59561849	A549	lung:	n/a	chr15:59561394-59561403
6	EP300	chr15:59560850-59561754	A549	lung:	n/a	chr15:59561395-59561404 chr15:59561394-59561403
7	FOSL1	chr15:59560310-59561757	HCT-116	colon:	n/a	chr15:59560573-59560582 chr15:59560654-59560663 chr15:59561393-59561405 chr15:59561395-59561404 chr15:59561394-59561403 chr15:59561395-59561402 chr15:59560656-59560663 chr15:59560648-59560660 chr15:59561396-59561407 chr15:59561395-59561403
8	JUN	chr15:59560385-59561762	Hela-S3	cervix:	n/a	chr15:59560573-59560582 chr15:59560654-59560663 chr15:59561393-59561405 chr15:59561395-59561404 chr15:59561394-59561403 chr15:59561395-59561402 chr15:59560656-59560663 chr15:59560648-59560660 chr15:59561396-59561407 chr15:59561395-59561403
9	CBX3	chr15:59561190-59561799	HCT-116	colon:	n/a	n/a
10	MAX	chr15:59561073-59561789	A549	lung:	n/a	chr15:59561394-59561403
11	FOSL2	chr15:59560397-59561838	A549	lung:	n/a	chr15:59560573-59560582 chr15:59560654-59560663 chr15:59561393-59561405 chr15:59561395-59561404 chr15:59561394-59561403 chr15:59561395-59561402 chr15:59560656-59560663 chr15:59560648-59560660 chr15:59561396-59561407 chr15:59561395-59561403
12	POLR2A	chr15:59560911-59561745	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr15:59560864-59561859	A549	lung:	n/a	chr15:59561396-59561405

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59561146..59562823-chr15:59949552..59951074,2	K562	blood:
2	chr15:59559608..59563212-chr15:59663665..59667768,4	MCF-7	breast:

Variant related genes	Relation type
MYO1E	TF binding region
ENSG00000157483	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000157470	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12437559	0.94[CEU][hapmap]
rs12439560	0.93[CEU][hapmap]
rs12443291	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12591694	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12595001	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917076	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs17236495	0.94[CEU][hapmap];0.87[TSI][hapmap]
rs17236502	0.94[CEU][hapmap]
rs17236509	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306783	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs2306784	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs4077169	0.94[CEU][hapmap];0.82[TSI][hapmap]
rs4420472	0.94[CEU][hapmap]
rs58487017	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6494081	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs67959850	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166002	0.94[CEU][hapmap]
rs8031729	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs8039095	0.84[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12443328	HSP90AB4P	cis	cerebellum	SCAN

Chromatin state (count:81 , 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	chr15:59533400-59564000	Weak transcription	Ovary	ovary
11	chr15:59533400-59566800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:59540000-59568800	Weak transcription	Fetal Kidney	kidney
13	chr15:59541200-59566400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:59542400-59568200	Weak transcription	Gastric	stomach
15	chr15:59542600-59563000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:59542800-59565400	Weak transcription	Left Ventricle	heart
17	chr15:59543200-59568200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:59544000-59566200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:59544600-59582400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:59547400-59564000	Weak transcription	Fetal Stomach	stomach
21	chr15:59547400-59587000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:59548200-59566400	Weak transcription	Aorta	Aorta
23	chr15:59548200-59567800	Weak transcription	Fetal Heart	heart
24	chr15:59550000-59568000	Weak transcription	Colonic Mucosa	Colon
25	chr15:59550000-59571600	Weak transcription	Esophagus	oesophagus
26	chr15:59550200-59566000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr15:59550600-59574600	Weak transcription	Adipose Nuclei	Adipose
28	chr15:59551400-59566200	Weak transcription	HSMMtube	muscle
29	chr15:59552000-59569800	Weak transcription	Brain Anterior Caudate	brain
30	chr15:59552600-59564000	Strong transcription	GM12878-XiMat	blood
31	chr15:59552600-59566400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:59554800-59562800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:59557600-59565200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:59557600-59566400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:59558200-59561800	Enhancers	HMEC	breast
36	chr15:59558400-59563600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:59558400-59564400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:59558600-59563600	Weak transcription	Liver	Liver
39	chr15:59558600-59565400	Weak transcription	Stomach Mucosa	stomach
40	chr15:59558800-59563800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:59558800-59565600	Weak transcription	HepG2	liver
42	chr15:59559600-59562000	Genic enhancers	NHEK	skin
43	chr15:59559800-59563600	Weak transcription	Brain Angular Gyrus	brain
44	chr15:59559800-59567600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:59559800-59568200	Weak transcription	Placenta	Placenta
46	chr15:59560000-59561800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:59560000-59561800	Enhancers	HUVEC	blood vessel
48	chr15:59560600-59562200	Transcr. at gene 5' and 3'	A549	lung
49	chr15:59560600-59563600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:59560600-59563600	Weak transcription	Brain Inferior Temporal Lobe	brain

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