Variant report

Variant	rs3741476
Chromosome Location	chr12:117672135-117672136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1047735	0.82[EUR][1000 genomes]
rs10774908	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10774910	0.96[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10850804	0.81[EUR][1000 genomes]
rs1093329	0.80[GIH][hapmap]
rs1093330	0.83[GIH][hapmap]
rs11068426	0.82[EUR][1000 genomes]
rs11068428	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs12830203	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2006789	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2291908	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs2293046	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7303718	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7959232	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs845820	0.83[GIH][hapmap]
rs904658	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]
rs9658420	0.80[EUR][1000 genomes]
rs9658498	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]

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
rs3741476	SRRM4	cis	parietal	SCAN

Chromatin state (count:14 , 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	chr12:117664800-117672400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:117665600-117672200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:117665600-117672400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:117666200-117704200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:117670000-117687800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:117671200-117674200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:117671600-117672600	Strong transcription	NHEK	skin
11	chr12:117671800-117673000	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:117671800-117673200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:117672000-117673000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:117672000-117673200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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