Variant report

Variant	rs11120002
Chromosome Location	chr1:212889867-212889868
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10863990	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10863993	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10863999	0.88[EUR][1000 genomes]
rs10864000	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs10864001	0.96[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs11120011	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11120012	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11120019	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11120024	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11120025	0.91[ASW][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs11120027	0.80[ASW][hapmap];0.82[CHD][hapmap];0.93[YRI][hapmap]
rs12097897	0.90[EUR][1000 genomes]
rs12119821	0.92[ASN][1000 genomes]
rs12125321	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12126017	0.90[EUR][1000 genomes]
rs12132316	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12136046	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12136834	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12239975	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12725274	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12727790	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741704	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12743402	0.82[EUR][1000 genomes]
rs12747251	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12758602	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12759287	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34274815	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3820679	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4951457	0.80[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs4951460	0.99[ASN][1000 genomes]
rs4951463	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4951636	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951637	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540761	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6540763	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6661720	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6669492	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6679350	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6679549	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6690689	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6694452	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6700410	0.88[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs6702025	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6702611	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7556272	0.90[AFR][1000 genomes];0.90[EUR][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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11120002	C1orf48	cis	multi-tissue	Pritchard
rs11120002	NSL1	cis	parietal	SCAN
rs11120002	LQK1	cis	parietal	SCAN
rs11120002	LOC642946	cis	multi-tissue	Pritchard
rs11120002	VASH2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212886400-212891800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:212886400-212894400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:212886600-212894400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links