Variant report

Variant	rs10116799
Chromosome Location	chr9:116184307-116184308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116178873..116180669-chr9:116183451..116186283,2	MCF-7	breast:
2	chr9:116149427..116152233-chr9:116182929..116184530,2	K562	blood:
3	chr9:116175870..116178487-chr9:116183376..116185276,2	K562	blood:

Extended variants
information (count: 173 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs10125960	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10217341	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10481676	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10481677	0.86[EUR][1000 genomes]
rs10981789	0.91[EUR][1000 genomes]
rs10981803	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10981807	0.86[EUR][1000 genomes]
rs10981808	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10981814	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10981816	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10981817	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10981819	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10981820	0.86[EUR][1000 genomes]
rs10981821	0.86[EUR][1000 genomes]
rs10981825	0.89[EUR][1000 genomes]
rs10981826	0.89[EUR][1000 genomes]
rs10981827	0.89[EUR][1000 genomes]
rs10981828	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10981829	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10981831	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10981832	0.85[EUR][1000 genomes]
rs12335716	0.91[EUR][1000 genomes]
rs12336719	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12337340	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12338588	0.86[EUR][1000 genomes]
rs12338697	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12338701	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12339493	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12339501	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12339617	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12340996	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12341332	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs12341490	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12342508	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12342699	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12343129	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12343141	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12343940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12344334	0.89[EUR][1000 genomes]
rs12344578	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12345524	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12345968	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12346076	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12346087	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12346939	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12347895	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs12348214	0.89[EUR][1000 genomes]
rs12348239	0.87[EUR][1000 genomes]
rs12349661	0.89[EUR][1000 genomes]
rs12353541	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1890992	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2050865	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2050866	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs28594159	0.87[EUR][1000 genomes]
rs28694002	0.86[EUR][1000 genomes]
rs28714985	0.86[EUR][1000 genomes]
rs35270441	0.86[EUR][1000 genomes]
rs35358414	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35533905	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3983381	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs41301525	0.87[EUR][1000 genomes]
rs41305473	0.84[EUR][1000 genomes]
rs41313331	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4596719	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4979257	0.83[GIH][hapmap]
rs55676913	0.86[EUR][1000 genomes]
rs55696921	0.89[EUR][1000 genomes]
rs55777057	0.89[EUR][1000 genomes]
rs55805468	0.89[EUR][1000 genomes]
rs55931715	0.89[EUR][1000 genomes]
rs55977108	0.86[EUR][1000 genomes]
rs56155263	0.89[EUR][1000 genomes]
rs56276438	0.89[EUR][1000 genomes]
rs56390346	0.89[EUR][1000 genomes]
rs61749208	0.89[EUR][1000 genomes]
rs6478011	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6478012	0.83[GIH][hapmap]
rs6478016	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6478017	0.83[GIH][hapmap]
rs6478022	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6478023	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7018783	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7020623	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7021491	0.83[GIH][hapmap]
rs7021688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7023661	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7024445	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7024612	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7024996	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7025170	0.89[EUR][1000 genomes]
rs7025745	0.86[EUR][1000 genomes]
rs7026568	0.86[EUR][1000 genomes]
rs7026656	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7027024	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7027340	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7028327	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7029685	0.86[EUR][1000 genomes]
rs7032311	0.87[EUR][1000 genomes]
rs7037441	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7040031	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7041833	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7042290	0.86[EUR][1000 genomes]
rs7042695	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7043140	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7043571	0.89[EUR][1000 genomes]
rs7045347	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7046202	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7046427	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7047062	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7048208	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7048305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72760092	0.97[EUR][1000 genomes]
rs72760093	0.96[EUR][1000 genomes]
rs72760097	0.91[EUR][1000 genomes]
rs72761903	0.90[EUR][1000 genomes]
rs72761904	0.91[EUR][1000 genomes]
rs72761966	0.86[EUR][1000 genomes]
rs72761968	0.89[EUR][1000 genomes]
rs72761972	0.89[EUR][1000 genomes]
rs72761982	0.89[EUR][1000 genomes]
rs72761985	0.87[EUR][1000 genomes]
rs72761987	0.86[EUR][1000 genomes]
rs72761988	0.89[EUR][1000 genomes]
rs72761992	0.86[EUR][1000 genomes]
rs72761994	0.86[EUR][1000 genomes]
rs72761997	0.87[EUR][1000 genomes]
rs72762002	0.84[EUR][1000 genomes]
rs72763803	0.86[EUR][1000 genomes]
rs72763804	0.86[EUR][1000 genomes]
rs72763806	0.87[EUR][1000 genomes]
rs72763816	0.89[EUR][1000 genomes]
rs72763826	0.87[EUR][1000 genomes]
rs72763827	0.89[EUR][1000 genomes]
rs72763828	0.87[EUR][1000 genomes]
rs72763831	0.87[EUR][1000 genomes]
rs72763832	0.89[EUR][1000 genomes]
rs72763842	0.87[EUR][1000 genomes]
rs72763843	0.87[EUR][1000 genomes]
rs72763846	0.87[EUR][1000 genomes]
rs72763848	0.90[EUR][1000 genomes]
rs72763849	0.90[EUR][1000 genomes]
rs7848203	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7849841	0.89[EUR][1000 genomes]
rs7851718	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7853373	0.86[EUR][1000 genomes]
rs7853792	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7854197	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7855325	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7856515	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7857943	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7859047	0.91[EUR][1000 genomes]
rs7860673	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs7861248	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7863159	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7864645	0.89[EUR][1000 genomes]
rs7865364	0.87[EUR][1000 genomes]
rs7867353	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7870227	0.92[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7870265	0.83[GIH][hapmap]
rs7870451	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7871186	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7872084	0.82[EUR][1000 genomes]
rs7872192	0.89[EUR][1000 genomes]
rs7872283	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs867375	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs884899	0.87[EUR][1000 genomes]
rs9299215	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs944345	0.87[EUR][1000 genomes]
rs944346	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9657641	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9657658	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs9657659	0.92[CEU][hapmap];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10116799	C9orf43	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116174200-116187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:116180400-116186600	Weak transcription	Primary B cells from cord blood	blood
3	chr9:116182400-116186000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:116182800-116184600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:116183200-116186400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:116184200-116184400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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