Variant report

Variant	rs10810494
Chromosome Location	chr9:15947462-15947463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10283865	0.82[CEU][hapmap]
rs10738418	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738419	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738420	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10738421	0.81[EUR][1000 genomes]
rs10738422	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10756704	0.81[GIH][hapmap]
rs10756720	0.81[CHD][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10756721	0.86[EUR][1000 genomes]
rs10756722	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10756723	0.85[AFR][1000 genomes]
rs10756724	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756725	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10756726	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756728	0.82[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10756729	0.82[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10756730	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10756731	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10756733	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10810439	0.82[ASW][hapmap];0.81[MKK][hapmap]
rs10810461	0.82[ASW][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap]
rs10810479	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10810480	0.86[EUR][1000 genomes]
rs10810481	0.86[EUR][1000 genomes]
rs10810482	0.85[EUR][1000 genomes]
rs10810483	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10810484	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs10810485	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10810486	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10810487	0.96[CEU][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10810488	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10810497	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10810498	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10810501	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810502	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810503	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810505	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810506	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810507	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810508	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810509	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810510	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10810514	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10962142	0.81[MKK][hapmap]
rs10962225	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10962227	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10962244	0.85[AFR][1000 genomes]
rs10962256	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12379234	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1328273	0.81[EUR][1000 genomes]
rs1328274	0.81[EUR][1000 genomes]
rs1328283	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs13297383	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1410444	0.92[CEU][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1410445	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1410446	0.85[EUR][1000 genomes]
rs1590749	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1590750	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1887664	0.85[EUR][1000 genomes]
rs1891211	0.82[CEU][hapmap]
rs1891212	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs1927697	0.85[EUR][1000 genomes]
rs1927698	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1984246	0.86[TSI][hapmap]
rs2182936	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2225182	0.81[CHB][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2891003	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3824502	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4146291	0.82[ASW][hapmap];0.81[GIH][hapmap];0.91[MKK][hapmap]
rs4472620	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4582646	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4740624	0.82[ASW][hapmap];0.84[MKK][hapmap]
rs4740629	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4741545	0.82[ASW][hapmap];0.95[MKK][hapmap]
rs4741546	0.91[MKK][hapmap]
rs4741548	0.88[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs4741552	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4741553	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4961433	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4961526	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7027202	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs769151	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[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961117	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9969685	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9969791	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9969816	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9969817	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753625	chr9:15914055-15980320	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
3	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3483970	chr9:15944147-15948125	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	esv3483971	chr9:15944147-15948125	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10810494	C9orf93	cis	parietal	SCAN
rs10810494	C9orf93	cis	cerebellum	SCAN
rs10810494	TTC39B	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15933200-15951400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:15943800-15954800	Weak transcription	Fetal Lung	lung
3	chr9:15946800-15947800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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