Variant report

Variant	rs9658498
Chromosome Location	chr12:117668525-117668526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1047735	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs10774908	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774910	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10850804	0.82[EUR][1000 genomes]
rs10850805	0.80[EUR][1000 genomes]
rs1093329	0.86[GIH][hapmap];0.87[MEX][hapmap]
rs1093330	0.89[GIH][hapmap]
rs11068426	0.81[EUR][1000 genomes]
rs11068428	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12830203	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2006789	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291908	0.80[CEU][hapmap];0.80[MEX][hapmap];0.83[EUR][1000 genomes]
rs2293046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2682825	0.82[GIH][hapmap]
rs3741476	1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7303718	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959232	0.80[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs816353	0.82[GIH][hapmap]
rs816362	0.83[ASN][1000 genomes]
rs816363	0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs845820	0.89[GIH][hapmap]
rs904658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv510592	chr12:117618872-117684713	Bivalent/Poised TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9658498	SRRM4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117651800-117696000	Weak transcription	Brain Anterior Caudate	brain
2	chr12:117658200-117678200	Weak transcription	Pancreas	Pancrea
3	chr12:117660000-117727400	Weak transcription	Psoas Muscle	Psoas
4	chr12:117661000-117669800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:117662200-117670400	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:117664800-117672400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:117665600-117672200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:117665600-117672400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:117666200-117704200	Weak transcription	Brain Angular Gyrus	brain
10	chr12:117667200-117668800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:117667200-117671600	Weak transcription	NHEK	skin
12	chr12:117668400-117669000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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