Variant report

Variant	rs1566106
Chromosome Location	chr5:178346215-178346216
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10039708	0.89[EUR][1000 genomes]
rs11249600	0.82[JPT][hapmap]
rs11948175	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11948664	0.91[EUR][1000 genomes]
rs11948690	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11949180	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11949181	0.90[EUR][1000 genomes]
rs11949892	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11949941	0.89[EUR][1000 genomes]
rs11950641	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11950746	0.91[EUR][1000 genomes]
rs11952790	0.89[EUR][1000 genomes]
rs11952817	0.82[JPT][hapmap]
rs11954382	0.92[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11955047	0.89[EUR][1000 genomes]
rs11958887	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11958941	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11960942	0.91[EUR][1000 genomes]
rs12186577	0.89[CHB][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap]
rs12186584	0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12187167	0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12553	0.94[EUR][1000 genomes]
rs12652691	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs12653128	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs12654454	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12654969	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs17664194	0.87[TSI][hapmap]
rs35030686	0.82[ASN][1000 genomes]
rs35609799	0.91[EUR][1000 genomes]
rs35957383	0.91[EUR][1000 genomes]
rs56814168	0.91[EUR][1000 genomes]
rs56872885	0.89[EUR][1000 genomes]
rs56951084	0.89[EUR][1000 genomes]
rs57153194	0.95[EUR][1000 genomes]
rs57426447	1.00[EUR][1000 genomes]
rs58354049	0.89[EUR][1000 genomes]
rs58554591	0.91[EUR][1000 genomes]
rs58672680	0.89[EUR][1000 genomes]
rs58679434	0.89[EUR][1000 genomes]
rs58941917	0.91[EUR][1000 genomes]
rs59242428	0.89[EUR][1000 genomes]
rs59736551	0.85[EUR][1000 genomes]
rs59829327	0.96[EUR][1000 genomes]
rs59849584	0.81[EUR][1000 genomes]
rs59994898	0.89[EUR][1000 genomes]
rs60178472	0.89[EUR][1000 genomes]
rs60277514	0.89[EUR][1000 genomes]
rs60417551	0.89[EUR][1000 genomes]
rs60601817	0.89[EUR][1000 genomes]
rs60813042	0.89[EUR][1000 genomes]
rs61295075	0.91[EUR][1000 genomes]
rs61310482	0.89[EUR][1000 genomes]
rs61492890	0.96[EUR][1000 genomes]
rs61744382	0.81[EUR][1000 genomes]
rs62395084	0.81[EUR][1000 genomes]
rs6600991	0.96[EUR][1000 genomes]
rs6859174	0.94[EUR][1000 genomes]
rs6861717	0.93[EUR][1000 genomes]
rs6862829	0.92[CEU][hapmap]
rs6863160	0.96[EUR][1000 genomes]
rs6863202	0.93[EUR][1000 genomes]
rs6863603	0.94[EUR][1000 genomes]
rs6865216	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs6866591	0.96[EUR][1000 genomes]
rs6870926	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs6877663	0.91[EUR][1000 genomes]
rs6878353	0.94[EUR][1000 genomes]
rs6882396	0.91[EUR][1000 genomes]
rs6883566	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6887256	0.91[EUR][1000 genomes]
rs6890083	0.95[EUR][1000 genomes]
rs6894878	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6895371	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs7448421	0.82[JPT][hapmap]
rs7706558	0.94[EUR][1000 genomes]
rs7724141	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7729560	0.90[EUR][1000 genomes]
rs7729717	0.90[EUR][1000 genomes]
rs7731067	0.94[EUR][1000 genomes]

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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv600464	chr5:178344648-178350709	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv600465	chr5:178344648-178352002	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv600466	chr5:178344648-178352245	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv600467	chr5:178344648-178352820	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv600468	chr5:178344648-178353156	Weak transcription ZNF genes & repeats Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv819936	chr5:178345813-178351240	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv823354	chr5:178345876-178351699	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv821324	chr5:178345876-178353585	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv823355	chr5:178346031-178351699	Weak transcription ZNF genes & repeats Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1566106	CNOT6	cis	cerebellum	SCAN
rs1566106	MGAT4B	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335600-178349000	ZNF genes & repeats	Liver	Liver
2	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr5:178341600-178347000	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr5:178341600-178347200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
5	chr5:178341600-178367000	ZNF genes & repeats	Fetal Brain Female	brain
6	chr5:178342000-178348200	Weak transcription	Right Ventricle	heart
7	chr5:178343000-178367200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr5:178343800-178348000	Weak transcription	Brain Angular Gyrus	brain
9	chr5:178344800-178346400	Strong transcription	Brain Substantia Nigra	brain
10	chr5:178345000-178346600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:178345400-178347200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:178345600-178346600	Weak transcription	Aorta	Aorta
13	chr5:178345600-178347600	Weak transcription	Fetal Kidney	kidney
14	chr5:178345600-178347800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:178345600-178348000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:178345600-178349400	Weak transcription	Primary T cells from cord blood	blood
17	chr5:178345800-178346600	Weak transcription	Ovary	ovary
18	chr5:178346000-178348000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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