Variant report

Variant	rs12990029
Chromosome Location	chr2:188967815-188967816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10175838	1.00[CHB][hapmap]
rs10180000	1.00[CHB][hapmap]
rs10209424	1.00[CHB][hapmap]
rs10460382	0.94[ASN][1000 genomes]
rs10469734	1.00[CHB][hapmap]
rs10931333	0.80[ASN][1000 genomes]
rs10931334	0.80[ASN][1000 genomes]
rs10931336	0.80[ASN][1000 genomes]
rs12465138	0.80[ASN][1000 genomes]
rs12478374	0.94[ASN][1000 genomes]
rs12615631	0.94[ASN][1000 genomes]
rs12693490	1.00[CHB][hapmap]
rs12693491	1.00[CHB][hapmap]
rs12693492	1.00[CHB][hapmap]
rs12693493	1.00[CHB][hapmap]
rs12987446	0.87[EUR][1000 genomes]
rs12992671	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12993224	0.87[ASN][1000 genomes]
rs13003972	1.00[CHB][hapmap]
rs13005325	0.80[ASN][1000 genomes]
rs13006933	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13015608	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13021054	0.94[ASN][1000 genomes]
rs13021984	0.94[ASN][1000 genomes]
rs13023212	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13024023	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs13027011	0.80[ASN][1000 genomes]
rs13027989	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13382200	1.00[CHB][hapmap]
rs13390401	1.00[CHB][hapmap]
rs13394232	1.00[CHB][hapmap]
rs13403228	1.00[CHB][hapmap]
rs13429075	1.00[CHB][hapmap]
rs1371517	0.80[ASN][1000 genomes]
rs1371518	0.80[ASN][1000 genomes]
rs1371527	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1371528	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1371529	0.94[ASN][1000 genomes]
rs1371530	1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1439894	0.80[ASN][1000 genomes]
rs1439898	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1439900	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1439901	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1439905	0.80[ASN][1000 genomes]
rs1439909	0.94[ASN][1000 genomes]
rs16829628	1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs16829631	0.87[EUR][1000 genomes]
rs16829839	0.94[ASN][1000 genomes]
rs2004888	1.00[CHB][hapmap]
rs2028374	0.94[ASN][1000 genomes]
rs2119091	0.80[ASN][1000 genomes]
rs2350563	0.94[ASN][1000 genomes]
rs34353529	1.00[CHB][hapmap]
rs34511378	0.89[EUR][1000 genomes]
rs34555222	0.80[ASN][1000 genomes]
rs34699014	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34836837	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35113537	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35311707	0.94[ASN][1000 genomes]
rs4427987	0.94[ASN][1000 genomes]
rs4535011	1.00[CHB][hapmap]
rs4666757	0.80[ASN][1000 genomes]
rs4667212	0.94[ASN][1000 genomes]
rs4667213	0.80[ASN][1000 genomes]
rs55755436	0.94[ASN][1000 genomes]
rs62180847	0.94[ASN][1000 genomes]
rs6434262	0.94[ASN][1000 genomes]
rs6707652	0.94[ASN][1000 genomes]
rs6707875	0.80[ASN][1000 genomes]
rs67082838	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712945	0.94[ASN][1000 genomes]
rs6718697	1.00[CHB][hapmap]
rs6723998	0.94[ASN][1000 genomes]
rs6742606	0.80[ASN][1000 genomes]
rs67732490	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67804711	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68028976	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72903888	0.87[EUR][1000 genomes]
rs72907984	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909886	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565935	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920408	0.94[ASN][1000 genomes]
rs9288151	1.00[CHB][hapmap]
rs9288152	1.00[CHB][hapmap]
rs971268	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9808523	1.00[CHB][hapmap]
rs9808557	1.00[CHB][hapmap]
rs997044	0.83[ASN][1000 genomes]
rs997045	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533353	chr2:188498301-189024655	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875602	chr2:188923773-189016215	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv875603	chr2:188923773-189025977	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584044	chr2:188928433-189016215	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002714	chr2:188934297-189025084	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv584045	chr2:188949715-189003106	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv875604	chr2:188957640-189043137	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv584046	chr2:188967163-189006890	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188944600-188988000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:188960200-188968000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links