Variant report

Variant	rs10962988
Chromosome Location	chr9:17269437-17269438
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10046851	0.81[CEU][hapmap]
rs10114662	0.82[CEU][hapmap]
rs10114688	0.82[CEU][hapmap]
rs10114730	0.81[CEU][hapmap]
rs10119370	0.82[CEU][hapmap]
rs10121841	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs10123715	0.82[CEU][hapmap]
rs10124487	0.82[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10738474	0.82[CEU][hapmap]
rs10756855	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756857	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10756858	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10756860	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10756867	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs10756869	0.82[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10756874	0.82[CEU][hapmap]
rs10756875	0.82[CEU][hapmap]
rs10756878	0.82[CEU][hapmap]
rs10810739	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10810740	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10810761	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10810764	0.82[CEU][hapmap]
rs10810765	0.81[CEU][hapmap]
rs10810773	0.82[CEU][hapmap]
rs10810782	0.92[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs10962947	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10962950	0.84[EUR][1000 genomes]
rs10962982	0.83[EUR][1000 genomes]
rs10963063	0.82[CEU][hapmap]
rs11560448	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12339564	0.83[EUR][1000 genomes]
rs12345267	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12379104	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13290922	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1372702	0.82[CEU][hapmap]
rs1442533	0.89[CEU][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs1576962	0.80[EUR][1000 genomes]
rs1582030	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1582031	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1583987	0.81[CEU][hapmap]
rs1591138	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1596193	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1759454	0.81[EUR][1000 genomes]
rs1759613	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1889114	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs1953105	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2044119	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs2099858	0.82[CEU][hapmap]
rs2151290	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2225598	0.82[CEU][hapmap]
rs2584535	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2584536	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2584547	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap]
rs2584554	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs2593382	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2593412	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2593414	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2779773	0.94[ASW][hapmap];0.82[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2779775	0.82[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2780197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2780198	1.00[CEU][hapmap]
rs2780199	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2780209	0.81[EUR][1000 genomes]
rs2780212	0.81[EUR][1000 genomes]
rs2815174	0.80[CHB][hapmap]
rs2990670	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs3780258	0.82[CEU][hapmap]
rs3824392	0.82[CEU][hapmap]
rs4246136	0.82[CEU][hapmap]
rs4272484	0.82[CEU][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs4409489	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4563978	0.80[EUR][1000 genomes]
rs4961437	0.82[CEU][hapmap]
rs4961539	0.82[CEU][hapmap]
rs4961544	0.82[CEU][hapmap]
rs4961545	0.82[CEU][hapmap]
rs4961547	0.82[CEU][hapmap]
rs4961552	0.82[CEU][hapmap]
rs4961555	0.81[CEU][hapmap]
rs593614	0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs595894	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs605916	0.83[EUR][1000 genomes]
rs619380	0.81[EUR][1000 genomes]
rs632265	0.81[EUR][1000 genomes]
rs645117	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6475139	0.81[CEU][hapmap]
rs6475141	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6475143	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs6475144	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs654521	0.82[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs670058	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs670511	0.83[EUR][1000 genomes]
rs7022060	0.94[ASW][hapmap];0.82[CEU][hapmap];0.83[TSI][hapmap]
rs7028779	0.81[CEU][hapmap]
rs7031133	0.81[CEU][hapmap]
rs7033974	0.83[EUR][1000 genomes]
rs7038186	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7041840	0.82[CEU][hapmap]
rs7046933	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs753393	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs7848397	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs7849084	0.81[CEU][hapmap]
rs7851890	0.82[CEU][hapmap]
rs7854724	0.82[CEU][hapmap]
rs7862069	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs7864650	0.82[EUR][1000 genomes]
rs7864919	0.82[CEU][hapmap]
rs7870101	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs7873708	0.82[CEU][hapmap]
rs870271	0.82[CEU][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9298774	0.82[CEU][hapmap]
rs9406666	0.83[EUR][1000 genomes]
rs9802710	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv892662	chr9:17168867-17329964	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1031269	chr9:17204320-17316969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv466270	chr9:17236376-17377629	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv613694	chr9:17236376-17377629	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv892663	chr9:17243746-17329964	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv892664	chr9:17250170-17296630	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv892665	chr9:17250170-17371690	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv892666	chr9:17256043-17280616	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv892667	chr9:17269437-17296630	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10962988	CNTLN	cis	parietal	SCAN
rs10962988	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17223600-17279400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:17262600-17280400	Weak transcription	Liver	Liver
3	chr9:17262800-17339800	Weak transcription	Left Ventricle	heart
4	chr9:17268600-17280000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:17269400-17269600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr9:17269400-17270000	Enhancers	HUES64 Cell Line	embryonic stem cell

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