Variant report

Variant	rs12913383
Chromosome Location	chr15:59043786-59043787
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59040055..59042151-chr15:59043208..59045709,2	MCF-7	breast:
2	chr15:59040077..59045685-chr15:59061303..59067063,14	K562	blood:
3	chr15:59040771..59044388-chr15:59046627..59050183,4	K562	blood:
4	chr15:59042046..59047020-chr15:59050998..59056418,7	K562	blood:
5	chr15:59040867..59044243-chr15:59224539..59228117,4	K562	blood:
6	chr15:59042171..59043978-chr15:59046627..59049380,3	K562	blood:

Variant related genes	Relation type
ENSG00000128923	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000200318	Chromatin interaction
ENSG00000137845	Chromatin interaction
ENSG00000245975	Chromatin interaction
ENSG00000259173	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11071393	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs11071397	0.94[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs12437457	0.87[GIH][hapmap];0.82[MEX][hapmap]
rs12437952	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12437998	0.80[AMR][1000 genomes]
rs12438487	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs12439231	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12439632	0.94[CEU][hapmap]
rs12440091	0.81[AMR][1000 genomes]
rs12441313	0.83[CEU][hapmap]
rs12441912	0.80[CEU][hapmap]
rs12442451	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs12442956	0.81[AMR][1000 genomes]
rs12591310	0.94[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs12592332	0.88[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs12594742	0.83[CEU][hapmap];0.87[MKK][hapmap]
rs12708455	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap]
rs12900343	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12905110	0.89[CEU][hapmap]
rs12906705	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap]
rs12906714	0.83[CEU][hapmap]
rs12907237	0.80[CEU][hapmap]
rs12908261	0.83[CEU][hapmap]
rs12910927	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12912286	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap]
rs12912327	0.80[AMR][1000 genomes]
rs12917083	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1426652	0.94[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1551445	0.94[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs16940587	0.95[CHB][hapmap]
rs16940589	0.95[CHB][hapmap]
rs16940647	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs16940651	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs17236194	0.83[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1820480	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2052804	0.85[AMR][1000 genomes]
rs2052805	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs2305421	0.90[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs2414608	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28455654	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs28470809	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28470867	0.82[EUR][1000 genomes]
rs28510910	0.85[EUR][1000 genomes]
rs28536555	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28576281	0.81[AMR][1000 genomes]
rs28724298	0.81[AMR][1000 genomes]
rs28733370	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28793354	0.83[EUR][1000 genomes]
rs35499736	0.85[AMR][1000 genomes]
rs544282	0.89[ASN][1000 genomes]
rs6494030	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap]
rs6494031	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap]
rs6494033	0.83[CEU][hapmap]
rs6494034	0.83[CEU][hapmap]
rs6494038	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7163733	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs7165019	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7165035	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7165402	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap]
rs7166076	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs7166325	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap]
rs7167528	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs7168825	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7169205	0.94[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7169796	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7170314	0.83[CEU][hapmap]
rs7171482	0.82[EUR][1000 genomes]
rs7174386	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs7174414	0.95[CHB][hapmap]
rs8029301	0.92[GIH][hapmap]
rs8029805	0.83[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs8033691	0.83[CEU][hapmap]
rs8036005	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs8039791	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap]
rs9302203	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs9635351	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9920720	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs9921024	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12913383	ONECUT1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59042000-59044400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:59042600-59062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:59042800-59043800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr15:59043000-59044000	Weak transcription	Placenta	Placenta
5	chr15:59043000-59044800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:59043000-59044800	Weak transcription	Thymus	Thymus
7	chr15:59043000-59045000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:59043000-59045000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:59043000-59046000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:59043000-59062400	Weak transcription	Psoas Muscle	Psoas
11	chr15:59043200-59044600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:59043200-59045000	Weak transcription	Fetal Thymus	thymus
13	chr15:59043200-59045600	Weak transcription	Liver	Liver
14	chr15:59043200-59045800	Weak transcription	K562	blood
15	chr15:59043200-59046200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:59043200-59046200	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:59043200-59046200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:59043200-59046600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:59043200-59047000	Weak transcription	Brain Substantia Nigra	brain
20	chr15:59043200-59047800	Weak transcription	Brain Anterior Caudate	brain
21	chr15:59043200-59048400	Weak transcription	A549	lung
22	chr15:59043400-59043800	Weak transcription	Primary T cells from cord blood	blood
23	chr15:59043600-59043800	Enhancers	HepG2	liver
24	chr15:59043600-59044800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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