Variant report

Variant	rs12988554
Chromosome Location	chr2:49040299-49040300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12986921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12987006	0.82[EUR][1000 genomes]
rs12988380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12991639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12991812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993218	0.82[EUR][1000 genomes]
rs12993342	0.81[EUR][1000 genomes]
rs12993350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12994449	0.82[EUR][1000 genomes]
rs12998973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12999088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13003416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13006849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13012154	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13013520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13026368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13026374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13033968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17555938	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17556008	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28407648	0.86[EUR][1000 genomes]
rs34096435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34139125	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34177801	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34246643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34316068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34375321	0.82[EUR][1000 genomes]
rs34493890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34519361	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34583302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34679037	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34747271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34790546	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34840154	0.82[EUR][1000 genomes]
rs34841582	0.82[EUR][1000 genomes]
rs34851917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34912705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35031960	0.82[EUR][1000 genomes]
rs35093053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35323371	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35625756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35775057	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35891136	0.82[EUR][1000 genomes]
rs35935449	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35944620	0.80[EUR][1000 genomes]
rs35975792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35988365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35989613	0.82[EUR][1000 genomes]
rs36028906	0.98[EUR][1000 genomes]
rs36098594	0.82[EUR][1000 genomes]
rs36139546	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4477968	0.82[EUR][1000 genomes]
rs59605770	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61037123	0.95[EUR][1000 genomes]
rs62137386	0.82[EUR][1000 genomes]
rs62137390	0.82[EUR][1000 genomes]
rs66479668	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66523169	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs66524960	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66593338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66709862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66713554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66898134	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67198598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67386139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67412822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67476091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71407521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71407527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71407528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71407529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71407530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71407531	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72811839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72811886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72823291	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv998864	chr2:49015878-49230000	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1014434	chr2:49016279-49053699	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1011016	chr2:49031921-49053699	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2763577	chr2:49035249-49053711	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv518963	chr2:49038154-49052293	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48994600-49080200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:49037200-49045400	Weak transcription	Ovary	ovary
3	chr2:49039200-49040400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:49039800-49043600	Weak transcription	Fetal Intestine Large	intestine
5	chr2:49040200-49040400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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