Variant report

Variant	rs2192439
Chromosome Location	chr12:9874226-9874227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 161 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs1008611	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10466762	1.00[JPT][hapmap]
rs10743820	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10743821	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743822	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10772005	1.00[JPT][hapmap]
rs10772006	1.00[JPT][hapmap]
rs10772060	1.00[CHB][hapmap]
rs10772104	1.00[JPT][hapmap]
rs10772119	1.00[JPT][hapmap]
rs10772120	1.00[JPT][hapmap]
rs10844350	1.00[JPT][hapmap]
rs10844351	1.00[JPT][hapmap]
rs10844359	1.00[JPT][hapmap]
rs10844372	1.00[JPT][hapmap]
rs10844418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs10844424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs10844429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs10844449	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10844457	0.89[ASN][1000 genomes]
rs10844476	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10844780	1.00[JPT][hapmap]
rs11052234	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs11052241	1.00[JPT][hapmap]
rs11052254	1.00[JPT][hapmap]
rs11052303	0.84[ASN][1000 genomes]
rs11052304	0.84[ASN][1000 genomes]
rs11052305	0.89[ASN][1000 genomes]
rs11052311	0.89[ASN][1000 genomes]
rs11052327	0.89[ASN][1000 genomes]
rs11052342	0.89[ASN][1000 genomes]
rs11052366	0.89[ASN][1000 genomes]
rs11052367	0.89[ASN][1000 genomes]
rs11052430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11052431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11052434	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11052718	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11052785	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11053051	1.00[JPT][hapmap]
rs11519377	0.89[ASN][1000 genomes]
rs11524523	0.89[ASN][1000 genomes]
rs12309762	0.89[ASN][1000 genomes]
rs12320830	0.89[ASN][1000 genomes]
rs12366653	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs12368445	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12369995	0.89[ASN][1000 genomes]
rs12370579	0.89[ASN][1000 genomes]
rs12371503	0.89[ASN][1000 genomes]
rs12371981	1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[ASN][1000 genomes]
rs12371982	0.89[ASN][1000 genomes]
rs12578698	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12578928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12582616	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12809752	0.89[ASN][1000 genomes]
rs12810851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12812783	0.89[ASN][1000 genomes]
rs12814560	0.89[ASN][1000 genomes]
rs12815393	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12816660	0.89[ASN][1000 genomes]
rs12817365	0.89[ASN][1000 genomes]
rs12817550	0.89[ASN][1000 genomes]
rs12817743	0.89[ASN][1000 genomes]
rs12818179	0.89[ASN][1000 genomes]
rs12819865	0.89[ASN][1000 genomes]
rs12820674	0.89[ASN][1000 genomes]
rs12823653	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12823699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12824491	1.00[JPT][hapmap]
rs12825507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12828602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12828773	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12830419	1.00[JPT][hapmap]
rs12830448	0.89[ASN][1000 genomes]
rs12830867	0.89[ASN][1000 genomes]
rs12830878	0.89[ASN][1000 genomes]
rs12831453	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1560008	1.00[JPT][hapmap]
rs16913477	1.00[JPT][hapmap]
rs1861089	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[ASN][1000 genomes]
rs1863871	1.00[JPT][hapmap]
rs1990533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[ASN][1000 genomes]
rs2114869	1.00[JPT][hapmap]
rs2114872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2114873	0.89[ASN][1000 genomes]
rs2192433	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2192434	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2192435	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2401396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2401397	1.00[JPT][hapmap]
rs2401398	1.00[JPT][hapmap]
rs3136577	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3176792	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs3176800	1.00[JPT][hapmap]
rs3176802	1.00[JPT][hapmap]
rs3176804	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3176806	1.00[JPT][hapmap]
rs3176807	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3176808	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34201389	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34279883	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34826829	0.89[ASN][1000 genomes]
rs35078787	0.89[ASN][1000 genomes]
rs35210729	0.92[AMR][1000 genomes]
rs35237063	0.89[ASN][1000 genomes]
rs35494990	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35512621	0.89[ASN][1000 genomes]
rs4763264	0.89[ASN][1000 genomes]
rs4763280	0.89[ASN][1000 genomes]
rs4763813	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs4763814	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4763819	0.89[ASN][1000 genomes]
rs4763835	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61913428	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6416258	1.00[JPT][hapmap]
rs6488065	1.00[JPT][hapmap]
rs6488109	0.89[ASN][1000 genomes]
rs6488122	0.89[ASN][1000 genomes]
rs66725265	0.89[ASN][1000 genomes]
rs67429242	0.89[ASN][1000 genomes]
rs704223	1.00[JPT][hapmap]
rs7132037	1.00[JPT][hapmap]
rs71441764	0.89[ASN][1000 genomes]
rs7302110	1.00[JPT][hapmap]
rs7302746	1.00[JPT][hapmap]
rs7304321	1.00[JPT][hapmap]
rs7304464	1.00[JPT][hapmap]
rs7309800	1.00[JPT][hapmap]
rs7310568	1.00[JPT][hapmap]
rs7310790	1.00[JPT][hapmap]
rs7310897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7311421	1.00[JPT][hapmap]
rs7311574	1.00[JPT][hapmap]
rs7311945	1.00[JPT][hapmap]
rs7312624	1.00[JPT][hapmap]
rs7485402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[ASN][1000 genomes]
rs7954062	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7961416	1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs7961812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs7961903	0.89[ASN][1000 genomes]
rs7962321	1.00[JPT][hapmap]
rs7969074	0.89[ASN][1000 genomes]
rs7972035	0.89[ASN][1000 genomes]
rs7974554	0.89[ASN][1000 genomes]
rs7974871	1.00[JPT][hapmap]
rs7975557	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[ASN][1000 genomes]
rs7975865	0.89[ASN][1000 genomes]
rs7978187	1.00[JPT][hapmap]
rs7979758	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs929615	1.00[JPT][hapmap]
rs9630264	0.89[ASN][1000 genomes]
rs9630265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9668568	0.89[ASN][1000 genomes]
rs982511	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9919786	1.00[JPT][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2192439	LOC374443	Cis_1M	lymphoblastoid	RTeQTL
rs2192439	CLEC2D	cis	multi-tissue	Pritchard
rs2192439	DCAL1	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:9872600-9875400	Enhancers	Fetal Lung	lung
5	chr12:9872600-9875600	Enhancers	HUVEC	blood vessel
6	chr12:9873200-9875400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:9873400-9874400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:9873400-9874400	Enhancers	Colon Smooth Muscle	Colon
9	chr12:9873400-9875000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:9873400-9875400	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:9873600-9874400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:9873600-9874400	Enhancers	NHEK	skin
13	chr12:9873600-9874600	Enhancers	Placenta	Placenta
14	chr12:9873600-9874800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr12:9873600-9875200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:9873600-9875400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:9873600-9875400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:9873600-9875400	Flanking Active TSS	A549	lung
19	chr12:9873600-9876800	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:9873600-9877600	Flanking Active TSS	GM12878-XiMat	blood
21	chr12:9874000-9874400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr12:9874000-9874400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:9874000-9874400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr12:9874000-9874400	Flanking Active TSS	Hela-S3	cervix
25	chr12:9874000-9874600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:9874000-9874600	Enhancers	HepG2	liver
27	chr12:9874000-9874800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:9874000-9874800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:9874000-9875000	Enhancers	Primary T cells from cord blood	blood
30	chr12:9874200-9874400	Enhancers	K562	blood
31	chr12:9874200-9874600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:9874200-9874800	Enhancers	Fetal Thymus	thymus
33	chr12:9874200-9874800	Weak transcription	Rectal Mucosa Donor 29	rectum

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