Variant report

Variant	rs12233479
Chromosome Location	chr3:112567789-112567790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112567751-112567805	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
CD200R1L	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10511314	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1054263	1.00[CEU][hapmap]
rs10934208	0.98[ASN][1000 genomes]
rs10934209	0.98[ASN][1000 genomes]
rs11543524	0.81[ASN][1000 genomes]
rs11916934	1.00[CEU][hapmap]
rs11920028	0.98[ASN][1000 genomes]
rs12233389	0.80[CHB][hapmap]
rs12233417	0.80[CHB][hapmap]
rs12233476	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233543	0.80[CHB][hapmap]
rs12233601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466873	0.80[CHB][hapmap]
rs1488188	0.80[CHB][hapmap]
rs16845095	0.80[CHB][hapmap]
rs16845097	0.80[CHB][hapmap]
rs16845099	0.80[CHB][hapmap]
rs16860078	1.00[CEU][hapmap]
rs16860145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16860233	0.80[CHB][hapmap]
rs16860236	0.80[CHB][hapmap]
rs16860239	0.80[CHB][hapmap]
rs16860245	0.80[CHB][hapmap]
rs16860272	0.80[CHB][hapmap]
rs16860279	0.80[YRI][hapmap]
rs16860319	1.00[CEU][hapmap]
rs2141347	0.80[CHB][hapmap]
rs4082660	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs4682435	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs56170322	0.84[EUR][1000 genomes]
rs56206000	0.98[ASN][1000 genomes]
rs56247644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56666099	0.98[ASN][1000 genomes]
rs56710227	0.98[ASN][1000 genomes]
rs56820451	0.95[ASN][1000 genomes]
rs57287136	0.93[ASN][1000 genomes]
rs57360909	0.95[ASN][1000 genomes]
rs58105957	0.98[ASN][1000 genomes]
rs59292601	0.98[ASN][1000 genomes]
rs60481719	0.99[ASN][1000 genomes]
rs60671920	0.98[ASN][1000 genomes]
rs60761581	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61191442	0.99[ASN][1000 genomes]
rs61526975	0.99[ASN][1000 genomes]
rs61674636	0.99[ASN][1000 genomes]
rs6764110	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs72491118	0.95[ASN][1000 genomes]
rs7628368	1.00[CEU][hapmap];1.00[MEX][hapmap]

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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112565600-112567800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:112565600-112568200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:112565800-112567800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:112565800-112568000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:112565800-112568200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr3:112565800-112569000	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:112566000-112568000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:112566000-112568200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:112566400-112567800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:112566400-112568000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:112566600-112567800	Enhancers	Dnd41	blood
12	chr3:112566600-112568400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:112567200-112567800	Enhancers	Primary T helper cells PMA-I stimulated	--

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