Variant report

Variant	rs10810461
Chromosome Location	chr9:15876507-15876508
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15876069..15878996-chr9:15881161..15882668,2	MCF-7	breast:

Extended variants
information (count: 154 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10283865	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10732335	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10733295	0.81[CEU][hapmap]
rs10733305	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10738417	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10738419	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs10738420	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10756690	0.92[CEU][hapmap]
rs10756697	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs10756704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10756709	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10756710	0.90[CHB][hapmap]
rs10756711	0.90[CHB][hapmap]
rs10756713	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10756714	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10756715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10756720	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs10756722	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10756724	0.84[CHB][hapmap]
rs10756726	0.82[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs10756728	0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap]
rs10756729	0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs10810426	0.81[CEU][hapmap]
rs10810427	0.81[CEU][hapmap]
rs10810428	0.92[CEU][hapmap];0.88[TSI][hapmap]
rs10810429	0.81[CEU][hapmap]
rs10810439	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10810442	0.81[CEU][hapmap]
rs10810446	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10810455	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10810462	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810474	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810475	0.82[ASN][1000 genomes]
rs10810479	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs10810483	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10810484	0.95[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap]
rs10810485	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10810486	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10810487	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10810488	0.82[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs10810494	0.82[ASW][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap]
rs10810501	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10810502	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs10810506	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10810509	0.82[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs10962126	0.81[CEU][hapmap]
rs10962142	0.84[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap]
rs10962149	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10962151	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs10962156	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10962157	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10962158	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10962212	0.82[ASN][1000 genomes]
rs10962215	0.82[ASN][1000 genomes]
rs10962225	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10962227	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11515071	0.80[ASN][1000 genomes]
rs11562188	0.95[EUR][1000 genomes]
rs12378499	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs12379234	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1328283	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1328286	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13287834	0.82[JPT][hapmap]
rs13292699	0.84[ASN][1000 genomes]
rs13296360	0.90[CHB][hapmap]
rs1341732	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1341737	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1341738	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1355171	0.81[CEU][hapmap]
rs1359952	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1396707	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs1396708	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs1410444	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1410445	0.81[ASN][1000 genomes]
rs1539172	0.90[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs1539173	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1592099	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs1891211	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1891212	0.85[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1927696	0.95[JPT][hapmap]
rs1927698	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1984246	0.89[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2105315	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2105317	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2105319	0.83[EUR][1000 genomes]
rs2182936	0.83[ASN][1000 genomes]
rs2185663	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2211323	0.83[EUR][1000 genomes]
rs2225181	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2225182	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2382534	0.89[CEU][hapmap]
rs2382540	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2382554	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987009	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2987010	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2987011	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2987012	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2987013	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2987014	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs3008666	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3008681	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3008747	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3008748	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3008749	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3008753	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4146290	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4146291	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4146293	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4472620	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4582646	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4740624	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4740627	0.95[EUR][1000 genomes]
rs4740628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4741534	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs4741535	0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap]
rs4741545	1.00[ASW][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs4741546	0.82[ASW][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap]
rs4741548	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4741552	0.82[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap]
rs4741553	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4961713	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6474954	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs6474966	0.81[CEU][hapmap]
rs6474967	0.84[ASW][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6474974	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap]
rs7024640	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs7027202	0.85[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7035863	0.84[CEU][hapmap]
rs7043770	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7045018	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs735962	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7466716	0.83[EUR][1000 genomes]
rs769151	0.82[ASW][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs7847144	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs7849380	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs7860528	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7860755	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7873776	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs950234	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs954663	0.81[CEU][hapmap]
rs955369	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs961117	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9886731	0.83[EUR][1000 genomes]
rs9969791	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv892633	chr9:15604746-15889411	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892635	chr9:15731775-15876507	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv892636	chr9:15794858-15876507	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv613667	chr9:15823667-15876507	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1015435	chr9:15841107-15880385	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1032081	chr9:15845902-15878115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1027790	chr9:15845902-15878841	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv969753	chr9:15873053-15877009	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10810461	C9orf93	cis	cerebellum	SCAN
rs10810461	C9orf93	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15857800-15885400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:15863600-15878200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:15874400-15876600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:15874600-15876600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:15874600-15876800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:15874600-15878400	Weak transcription	HSMMtube	muscle
7	chr9:15876400-15877400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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