Variant report

Variant	rs12489734
Chromosome Location	chr3:112566491-112566492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10511313	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10804504	0.84[CEU][hapmap]
rs10804505	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804506	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10934188	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10934191	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934197	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1114404	0.84[CEU][hapmap]
rs11714354	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11717778	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718878	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11720045	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12487198	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12490586	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12490671	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12633234	0.84[EUR][1000 genomes]
rs13063847	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076130	0.82[EUR][1000 genomes]
rs13092251	0.94[EUR][1000 genomes]
rs13094280	0.84[CEU][hapmap]
rs13323006	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1354055	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16860225	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1997281	0.84[CEU][hapmap]
rs2220397	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2399437	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2399442	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28782232	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34147006	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6763318	0.92[CEU][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765575	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786513	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787688	0.84[CEU][hapmap]
rs6795428	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6798395	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6799171	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6805341	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6806976	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807722	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6808135	0.84[CEU][hapmap];0.85[YRI][hapmap]
rs7609699	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7621490	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639603	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7641119	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7651207	0.84[CEU][hapmap]
rs9288959	0.84[CEU][hapmap]
rs9288964	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9813901	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9814008	0.84[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815002	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9819621	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9820561	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9823692	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9825873	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9826834	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829184	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834599	0.84[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838295	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9839592	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9842637	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845041	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9846377	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9852286	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9852577	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9853006	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9858931	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9860428	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9863580	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9865066	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868922	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9869058	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9871326	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9871605	0.85[CEU][hapmap]
rs9877803	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3501334	chr3:112546820-112648766	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3501335	chr3:112546820-112648766	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112565600-112566600	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:112565600-112567600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:112565600-112567800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:112565600-112568200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:112565800-112566800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:112565800-112567800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:112565800-112568000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:112565800-112568200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:112565800-112569000	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:112566000-112567400	Enhancers	Primary T cells from cord blood	blood
11	chr3:112566000-112568000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:112566000-112568200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:112566400-112566800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:112566400-112567200	Enhancers	Primary B cells from cord blood	blood
15	chr3:112566400-112567600	ZNF genes & repeats	GM12878-XiMat	blood
16	chr3:112566400-112567800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:112566400-112568000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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