Variant report

Variant	rs12437457
Chromosome Location	chr15:58877563-58877564
allele	C/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	RCOR1	chr15:58877259-58877587	K562	blood:	n/a	n/a
2	UBTF	chr15:58877255-58877812	K562	blood:	n/a	n/a
3	ZMIZ1	chr15:58877206-58877861	K562	blood:	n/a	n/a
4	RUNX3	chr15:58877563-58878606	GM12878	blood:	n/a	n/a
5	MAX	chr15:58876995-58877615	K562	blood:	n/a	n/a
6	POLR2A	chr15:58877150-58878766	A549	lung:	n/a	n/a
7	ZNF384	chr15:58877356-58877624	K562	blood:	n/a	n/a
8	UBTF	chr15:58877369-58877568	K562	blood:	n/a	n/a
9	POLR2A	chr15:58877039-58878602	HepG2	liver:	n/a	n/a
10	MYC	chr15:58877215-58877618	K562	blood:	n/a	n/a
11	NFIC	chr15:58877554-58878366	GM12878	blood:	n/a	n/a
12	REST	chr15:58877308-58877588	K562	blood:	n/a	n/a
13	MTA3	chr15:58877384-58878686	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:58877136-58878670	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:58877527-58877573	K562	blood:	n/a	n/a
16	POLR2A	chr15:58877084-58878767	K562	blood:	n/a	n/a
17	IKZF1	chr15:58877541-58878378	GM12878	blood:	n/a	n/a
18	JUND	chr15:58877309-58877586	K562	blood:	n/a	n/a
19	POLR2A	chr15:58876928-58878736	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:58877135-58878659	Hela-S3	cervix:	n/a	n/a
21	TAL1	chr15:58877293-58877657	K562	blood:	n/a	chr15:58877443-58877461
22	NFIC	chr15:58877532-58878367	GM12878	blood:	n/a	n/a
23	GATA2	chr15:58877259-58877604	K562	blood:	n/a	chr15:58877440-58877450 chr15:58877443-58877450 chr15:58877444-58877461

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58578437..58580327-chr15:58877282..58879701,2	K562	blood:

Variant related genes	Relation type
ENSG00000259250	TF binding region

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11071391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071392	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11071393	0.88[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12437998	0.81[AMR][1000 genomes]
rs12438487	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12438810	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12439231	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12440246	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12440267	0.84[AMR][1000 genomes]
rs12441313	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs12441912	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs12442451	0.94[CEU][hapmap];0.89[AMR][1000 genomes]
rs12591291	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12591543	0.83[EUR][1000 genomes]
rs12592332	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap]
rs12592750	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12594742	0.94[CEU][hapmap]
rs12708455	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs12901989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905110	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12905173	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12906705	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12906714	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907237	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908165	0.87[CEU][hapmap]
rs12908261	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs12908449	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12912286	0.88[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs12912327	0.84[AMR][1000 genomes]
rs12913383	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs12913969	0.81[CEU][hapmap]
rs12917500	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917577	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1426652	0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap]
rs16940587	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16940589	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16940647	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16940651	0.94[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17236194	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs17301864	0.88[CEU][hapmap]
rs17301905	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17301954	0.82[AMR][1000 genomes]
rs1820548	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2052805	0.88[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs2242063	0.82[CEU][hapmap]
rs2242066	0.82[CEU][hapmap]
rs2303532	0.80[AMR][1000 genomes]
rs2305421	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28417700	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28427123	0.84[AMR][1000 genomes]
rs28455654	0.86[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28457680	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28489732	0.84[AMR][1000 genomes]
rs28542491	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28569241	0.86[AFR][1000 genomes]
rs28573205	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28584993	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28600144	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28609304	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28678478	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28722857	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28818840	0.86[AMR][1000 genomes]
rs34793995	0.82[AMR][1000 genomes]
rs35499736	0.81[EUR][1000 genomes]
rs35956992	0.88[AMR][1000 genomes]
rs6074	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap]
rs6494030	0.94[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6494031	0.88[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6494033	0.94[CEU][hapmap]
rs6494034	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6494038	0.88[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7163733	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs7164620	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7165035	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7165402	0.94[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7166076	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7166325	0.94[CEU][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7167528	0.88[CEU][hapmap]
rs7170314	0.94[CEU][hapmap]
rs7174175	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7174386	0.94[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7174414	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7178954	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7180550	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8026668	0.82[EUR][1000 genomes]
rs8029805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs8033565	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8033691	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8036005	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8039791	0.89[CEU][hapmap];0.97[GIH][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs871804	1.00[ASW][hapmap];0.82[CEU][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap]
rs9302203	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9635351	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9744518	0.83[EUR][1000 genomes]
rs9920042	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9920310	0.80[AMR][1000 genomes]
rs9920720	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9921024	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12437457	HSP90AB4P	cis	cerebellum	SCAN
rs12437457	RNF111	cis	parietal	SCAN
rs12437457	PIGB	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58874600-58889200	Weak transcription	Small Intestine	intestine
2	chr15:58876600-58878600	Enhancers	HSMMtube	muscle
3	chr15:58876600-58878800	Enhancers	Fetal Thymus	thymus
4	chr15:58876600-58879200	Enhancers	Thymus	Thymus
5	chr15:58876800-58877600	Enhancers	GM12878-XiMat	blood
6	chr15:58876800-58878200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:58877000-58877800	Enhancers	Brain Substantia Nigra	brain
8	chr15:58877000-58878000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr15:58877000-58878000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr15:58877000-58878000	Enhancers	Left Ventricle	heart
11	chr15:58877000-58878000	Enhancers	Right Atrium	heart
12	chr15:58877000-58878600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr15:58877200-58877600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr15:58877200-58877600	Enhancers	Placenta	Placenta
15	chr15:58877200-58878000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr15:58877200-58878000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:58877200-58878000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:58877200-58878000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:58877200-58878000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:58877200-58878000	Flanking Active TSS	K562	blood
21	chr15:58877200-58878200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:58877200-58878200	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr15:58877200-58878400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:58877200-58878400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:58877200-58878600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:58877200-58878600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:58877200-58878600	Enhancers	Fetal Heart	heart
28	chr15:58877400-58877600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr15:58877400-58877800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr15:58877400-58877800	Enhancers	Fetal Intestine Large	intestine
31	chr15:58877400-58878200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr15:58877400-58878400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr15:58877400-58878600	Enhancers	Primary hematopoietic stem cells	blood
34	chr15:58877400-58881200	Weak transcription	HSMM	muscle

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