Variant report

Variant	rs10792121
Chromosome Location	chr11:57747402-57747403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10750876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10750878	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs10750880	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs10750882	0.82[CEU][hapmap]
rs10792119	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10792120	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10792122	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792126	0.82[ASN][1000 genomes]
rs10792128	0.82[ASN][1000 genomes]
rs10792129	0.82[ASN][1000 genomes]
rs10792130	0.85[GIH][hapmap]
rs10792135	0.82[CEU][hapmap]
rs10896663	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10896668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10896671	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896672	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896674	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896675	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896690	0.85[ASN][1000 genomes]
rs10896692	0.82[ASN][1000 genomes]
rs10896696	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11229194	0.87[AMR][1000 genomes]
rs11229195	0.84[AMR][1000 genomes]
rs11229221	0.84[ASN][1000 genomes]
rs11229247	0.82[CEU][hapmap]
rs11229250	0.82[CEU][hapmap]
rs1123307	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs11512733	0.83[AMR][1000 genomes]
rs12281690	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12363350	0.82[CEU][hapmap]
rs1317828	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1447169	0.82[CEU][hapmap]
rs1510419	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510421	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1848880	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1848882	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1848883	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1868043	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2003375	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2089748	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136726	0.92[EUR][1000 genomes]
rs2167358	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2441979	0.82[GIH][hapmap]
rs2513726	0.85[GIH][hapmap]
rs2513727	0.85[GIH][hapmap]
rs2514187	0.83[GIH][hapmap]
rs2866828	0.93[EUR][1000 genomes]
rs2866829	0.93[EUR][1000 genomes]
rs34243081	0.83[AMR][1000 genomes]
rs3974323	0.82[CEU][hapmap]
rs4272801	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4939170	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4939176	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs4939182	0.82[CEU][hapmap]
rs6591447	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6591455	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs7109726	0.82[CEU][hapmap]
rs7110748	0.82[CEU][hapmap]
rs7117711	0.81[CEU][hapmap]
rs7118536	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs7924376	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924454	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921133	0.82[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs921134	0.85[GIH][hapmap]
rs921135	0.85[GIH][hapmap]
rs938012	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs976429	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9794898	0.83[EUR][1000 genomes]
rs9795237	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv517822	chr11:57728993-57751001	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv328	chr11:57744748-57789940	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10792121	TIMM10	cis	parietal	SCAN
rs10792121	OR4C6	cis	parietal	SCAN
rs10792121	MS4A8B	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57742600-57751000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57742600-57751000	Weak transcription	Brain Germinal Matrix	brain
3	chr11:57745000-57748200	Enhancers	HSMMtube	muscle
4	chr11:57745400-57751200	Weak transcription	Left Ventricle	heart
5	chr11:57745600-57750200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:57745800-57750800	Weak transcription	Fetal Muscle Leg	muscle
7	chr11:57746200-57748000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:57746200-57748000	Enhancers	HSMM	muscle
9	chr11:57746800-57747800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:57747000-57749800	Enhancers	HepG2	liver
11	chr11:57747400-57747600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr11:57747400-57749600	Weak transcription	Pancreas	Pancrea

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