Variant report

Variant	rs12564080
Chromosome Location	chr1:86196586-86196587
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1047893	0.92[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs10493773	0.88[CEU][hapmap]
rs10493774	0.88[CEU][hapmap]
rs10873716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10873717	0.88[ASN][1000 genomes]
rs11161645	0.86[TSI][hapmap]
rs11161649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161650	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161654	0.88[ASN][1000 genomes]
rs11161656	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161657	0.88[ASN][1000 genomes]
rs11161658	0.88[ASN][1000 genomes]
rs11161659	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161660	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161661	0.88[ASN][1000 genomes]
rs11161662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161663	0.88[ASN][1000 genomes]
rs11161664	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161665	0.88[ASN][1000 genomes]
rs11161667	0.91[ASN][1000 genomes]
rs12058974	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12061951	0.92[LWK][hapmap]
rs12063702	0.91[ASN][1000 genomes]
rs12067749	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12075929	0.83[ASW][hapmap];0.96[CEU][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap]
rs12089500	0.87[ASN][1000 genomes]
rs12097932	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12566746	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs12738010	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12739713	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12752817	0.91[ASN][1000 genomes]
rs12754358	0.84[CEU][hapmap]
rs12756013	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12757270	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758511	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539444	0.87[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs1889919	0.88[ASN][1000 genomes]
rs1889920	0.88[ASN][1000 genomes]
rs2069208	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274738	0.88[CEU][hapmap]
rs2389972	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35438778	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3753786	0.92[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs3753789	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3753790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3767163	0.88[CEU][hapmap]
rs414618	0.92[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs6576784	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672312	0.92[ASW][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[ASN][1000 genomes]
rs6689168	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6697535	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs6698578	0.87[CEU][hapmap]
rs7518312	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520491	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7554844	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12564080	RPF1	cis	cerebellum	SCAN
rs12564080	ZNHIT6	cis	lymphoblastoid	seeQTL
rs12564080	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs12564080	ZNHIT6	cis	Artery Aorta	GTEx
rs12564080	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs12564080	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86191600-86210400	Weak transcription	Fetal Lung	lung
2	chr1:86194400-86196600	Strong transcription	Primary hematopoietic stem cells	blood
3	chr1:86194600-86197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:86195200-86202400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86196400-86205600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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