Variant report

Variant	rs1325260
Chromosome Location	chr1:86301450-86301451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1010058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10873722	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873723	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10873725	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161676	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11161677	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161678	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161682	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161684	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161685	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161686	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161687	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11579570	0.82[ASN][1000 genomes]
rs11590890	0.82[ASN][1000 genomes]
rs12077825	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12088004	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12091583	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12098168	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12119620	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122234	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12128605	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12136023	0.81[EUR][1000 genomes]
rs12145864	0.93[EUR][1000 genomes]
rs12727784	1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12727916	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12735553	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12745753	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12746325	1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12753056	0.82[ASN][1000 genomes]
rs12760458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1481199	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1564515	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1564517	0.82[AMR][1000 genomes]
rs1698733	0.85[MEX][hapmap]
rs1842579	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2297744	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4486475	0.81[MEX][hapmap]
rs4912437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912446	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605060	0.90[MEX][hapmap]
rs6576790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6576791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576792	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6677315	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6693669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697619	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698633	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7539262	0.82[ASN][1000 genomes]
rs861933	0.90[MEX][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	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	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1011293	chr1:86270649-86416972	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1325260	ZNHIT6	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86297000-86315400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:86297400-86303600	Weak transcription	GM12878-XiMat	blood
3	chr1:86300000-86305200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:86300400-86305000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:86300600-86302400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:86300600-86302800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:86301400-86301800	Strong transcription	Primary hematopoietic stem cells	blood
8	chr1:86301400-86301800	Strong transcription	Fetal Lung	lung

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