Variant report

Variant	rs852816
Chromosome Location	chr12:21849348-21849349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10770848	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10770851	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10841872	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10841873	0.84[EUR][1000 genomes]
rs10841874	0.86[EUR][1000 genomes]
rs10841878	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10841880	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10841886	0.82[ASN][1000 genomes]
rs10841887	0.82[ASN][1000 genomes]
rs10841888	0.82[ASN][1000 genomes]
rs10841889	0.82[ASN][1000 genomes]
rs10841890	0.82[ASN][1000 genomes]
rs11046148	0.86[EUR][1000 genomes]
rs11046149	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11046150	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11046151	0.86[EUR][1000 genomes]
rs11046153	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11046154	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11046156	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11046157	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11046158	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11046159	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11046160	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11046161	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11046164	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11046166	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046171	0.82[ASN][1000 genomes]
rs11046172	0.82[ASN][1000 genomes]
rs11046173	0.82[ASN][1000 genomes]
rs11046174	0.82[ASN][1000 genomes]
rs11836830	0.83[EUR][1000 genomes]
rs12426310	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12426826	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12816929	0.82[ASN][1000 genomes]
rs12824571	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12824788	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs12824936	0.85[EUR][1000 genomes]
rs12825320	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12826014	0.85[EUR][1000 genomes]
rs12829701	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12830306	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1293188	0.82[ASN][1000 genomes]
rs153941	0.90[CHB][hapmap]
rs1586844	0.82[ASN][1000 genomes]
rs1650307	0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap]
rs1677091	0.81[CHB][hapmap]
rs16924224	0.86[ASW][hapmap]
rs17629491	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2077105	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34015001	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34031159	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34084105	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34822889	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58134911	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60462572	0.85[EUR][1000 genomes]
rs66592830	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66978947	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67247140	0.82[EUR][1000 genomes]
rs67286733	0.83[EUR][1000 genomes]
rs7133519	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135965	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297042	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301852	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301883	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7302534	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7302639	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7303185	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7303528	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7303612	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7303644	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305475	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73077300	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7316427	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316475	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316669	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7953579	0.91[CHB][hapmap]
rs7975931	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs852815	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv469164	chr12:21688900-21966701	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv557744	chr12:21688900-21966701	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv832349	chr12:21749093-21930695	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs852816	RP11-59N23.3	cis	lung	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21844800-21852600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:21845000-21850600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:21845200-21852600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:21845400-21851000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:21848200-21849400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:21848400-21850000	Enhancers	Osteobl	bone
7	chr12:21848400-21850400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:21848400-21851000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:21848600-21850400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:21849000-21849800	Enhancers	Fetal Lung	lung
11	chr12:21849000-21850000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:21849000-21851600	Enhancers	NHDF-Ad	bronchial
13	chr12:21849200-21849400	Enhancers	Fetal Stomach	stomach
14	chr12:21849200-21849600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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