Variant report

Variant	rs7860339
Chromosome Location	chr9:15543074-15543075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr9:15543071-15543382	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr9:15543068-15543387	IMR90	lung:	n/a	n/a
3	FOSL2	chr9:15543071-15543642	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15540944..15543831-chr9:15548082..15550784,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-246P	TF binding region

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10116904	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117524	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118595	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118675	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118719	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10119257	0.87[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119931	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120171	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121012	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121911	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121971	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123084	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124655	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10124718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124746	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125713	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1041529	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962054	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962061	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336383	1.00[ASN][1000 genomes]
rs12336445	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337310	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344963	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348561	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348564	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348780	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350062	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350903	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352398	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12353048	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355172	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1472941	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs1553727	0.83[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs175762	1.00[ASN][1000 genomes]
rs1882939	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs202321	1.00[ASN][1000 genomes]
rs2055774	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2064030	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2202865	1.00[ASN][1000 genomes]
rs2382536	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2665503	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs2665510	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2665511	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2665512	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2665515	0.83[GIH][hapmap];1.00[ASN][1000 genomes]
rs2737836	0.88[AMR][1000 genomes]
rs2737840	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276434	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs276437	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276438	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276439	1.00[ASN][1000 genomes]
rs276440	1.00[ASN][1000 genomes]
rs276442	1.00[ASN][1000 genomes]
rs276445	1.00[ASN][1000 genomes]
rs276446	1.00[ASN][1000 genomes]
rs276450	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276451	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276452	0.80[EUR][1000 genomes]
rs2777951	1.00[ASN][1000 genomes]
rs2795123	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2795124	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2795125	1.00[ASN][1000 genomes]
rs2795127	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2795128	1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821525	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821529	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821530	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2821533	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2821542	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821543	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821544	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449490	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28497163	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610358	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28735068	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28796681	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28800775	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28805077	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28808908	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28844368	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28882210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28893033	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3119700	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122701	1.00[ASN][1000 genomes]
rs3122705	1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129711	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365710	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381205	1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392627	1.00[ASN][1000 genomes]
rs398117	1.00[ASN][1000 genomes]
rs398178	1.00[ASN][1000 genomes]
rs399808	1.00[ASN][1000 genomes]
rs401393	1.00[ASN][1000 genomes]
rs413356	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415157	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418153	1.00[ASN][1000 genomes]
rs424131	1.00[ASN][1000 genomes]
rs443563	1.00[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4741537	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs592452	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6474941	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6474949	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6474957	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs7021840	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035422	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs741930	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs7852936	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870315	0.86[ASW][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs796391	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811282	1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909323	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs926154	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298729	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9406518	1.00[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	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	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
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7860339	C9orf93	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15542000-15543800	Enhancers	Fetal Stomach	stomach
2	chr9:15542200-15544000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr9:15542600-15543600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr9:15542800-15543800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr9:15543000-15543200	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links