Variant report

Variant	rs11957963
Chromosome Location	chr5:35753715-35753716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10037564	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10043724	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap]
rs10043734	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10044393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941258	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs10941260	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12697350	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2201410	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs4869462	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4869464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4869623	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62353695	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451213	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6451217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6875940	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs6891098	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs716971	0.83[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs7443063	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7447153	0.84[CHB][hapmap]
rs7705904	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7710255	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11957963	RICTOR	cis	parietal	SCAN
rs11957963	LAG3	trans	lymphoblastoid	seeQTL
rs11957963	LOC149134	trans	parietal	SCAN
rs11957963	UGT3A2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35753400-35754600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
2	chr5:35753400-35755000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr5:35753400-35755200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:35753600-35754200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:35753600-35754200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:35753600-35754200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr5:35753600-35754800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr5:35753600-35755400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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