Variant report

Variant	rs904658
Chromosome Location	chr12:117665544-117665545
allele	G/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:21)

rs_ID	r²[population]
rs1047735	0.80[CEU][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs10774908	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774910	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10850804	0.82[EUR][1000 genomes]
rs10850805	0.80[EUR][1000 genomes]
rs1093329	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs1093330	0.83[GIH][hapmap]
rs11068426	0.81[EUR][1000 genomes]
rs11068428	0.80[CEU][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs12830203	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2006789	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291908	0.80[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs2293046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741476	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7303718	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959232	1.00[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs816353	0.84[GIH][hapmap]
rs816362	0.84[ASN][1000 genomes]
rs816363	0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs845820	0.83[GIH][hapmap]
rs9658498	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:3 , 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
3	esv3418890	chr12:117665132-117665562	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs904658	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	chr12:117660400-117667200	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:117661000-117669800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:117662200-117670400	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:117662600-117667200	Strong transcription	NHEK	skin
8	chr12:117664400-117665600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:117664400-117666400	Enhancers	A549	lung
10	chr12:117664800-117672400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:117665400-117665600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:117665400-117668400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links