Variant report

Variant	rs12812783
Chromosome Location	chr12:9867339-9867340
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10772060	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10844418	1.00[CHB][hapmap]
rs10844424	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs10844429	1.00[CHB][hapmap]
rs10844449	1.00[AFR][1000 genomes]
rs10844476	1.00[AFR][1000 genomes]
rs11052327	1.00[AFR][1000 genomes]
rs11052342	1.00[AFR][1000 genomes]
rs11052430	1.00[CHB][hapmap]
rs11052431	1.00[CHB][hapmap]
rs11052434	1.00[AFR][1000 genomes]
rs11052718	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs11519377	1.00[AFR][1000 genomes]
rs11524523	1.00[AFR][1000 genomes]
rs12369995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371503	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371981	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12578928	1.00[CHB][hapmap]
rs12582616	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12809752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810851	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12814560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815393	1.00[AFR][1000 genomes]
rs12816660	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817365	1.00[AFR][1000 genomes]
rs12817550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823699	1.00[CHB][hapmap]
rs12825507	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12828602	1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs12828773	1.00[AFR][1000 genomes]
rs12830448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2080207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2114872	1.00[CHB][hapmap]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs34623781	0.89[ASN][1000 genomes]
rs34826829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34850016	0.89[AFR][1000 genomes]
rs35078787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35237063	1.00[AFR][1000 genomes]
rs35512621	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763280	1.00[ASN][1000 genomes]
rs4763813	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4763814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763819	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs66725265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67429242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71441764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310897	1.00[CHB][hapmap]
rs7485402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7954062	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7961812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961903	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7969074	1.00[AFR][1000 genomes]
rs7974554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	1.00[CHB][hapmap]
rs982511	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv442255	chr12:9862078-9874924	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3693109	chr12:9863968-9876091	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv8910	chr12:9865993-9872509	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12812783	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9858000-9872200	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:9859000-9870200	Enhancers	Primary B cells from cord blood	blood
3	chr12:9861000-9873200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
5	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:9861800-9868200	Enhancers	GM12878-XiMat	blood
7	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:9864000-9873600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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