Variant report

Variant	rs2453166
Chromosome Location	chr12:105203528-105203529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs1038968	0.88[EUR][1000 genomes]
rs10507184	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1070316	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs10746008	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10778358	0.86[ASW][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs1155994	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1316594	0.94[EUR][1000 genomes]
rs1389609	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1389612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474459	0.89[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1565813	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1565815	0.93[EUR][1000 genomes]
rs2047124	0.88[EUR][1000 genomes]
rs2131806	0.89[CEU][hapmap];0.84[GIH][hapmap]
rs2141248	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245927	0.94[EUR][1000 genomes]
rs2245931	0.94[EUR][1000 genomes]
rs2248012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249454	0.86[ASW][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs2453154	0.94[CEU][hapmap];0.80[GIH][hapmap]
rs2453155	0.94[CEU][hapmap];0.91[GIH][hapmap]
rs2453156	0.94[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2453157	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453158	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2453160	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453161	0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2453167	0.94[EUR][1000 genomes]
rs2453168	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2463016	0.94[EUR][1000 genomes]
rs2463017	0.94[EUR][1000 genomes]
rs2463018	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2463025	0.94[EUR][1000 genomes]
rs2463429	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2463431	0.88[EUR][1000 genomes]
rs2463432	0.93[EUR][1000 genomes]
rs2463433	0.94[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs2463441	0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2463442	0.84[CEU][hapmap]
rs2463443	0.84[CEU][hapmap]
rs2463444	0.84[CEU][hapmap]
rs2468083	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468089	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2468090	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2468099	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468100	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468105	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468109	0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2468110	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2468112	0.83[EUR][1000 genomes]
rs2468340	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2565167	0.94[EUR][1000 genomes]
rs2642110	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2642116	0.94[EUR][1000 genomes]
rs2730291	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs2730295	0.89[EUR][1000 genomes]
rs2731030	0.89[EUR][1000 genomes]
rs4334113	0.84[ASN][1000 genomes]
rs4388976	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4393404	0.86[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6539167	0.88[EUR][1000 genomes]
rs6539170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6539171	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs703681	0.89[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs7135015	0.86[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7138686	0.86[ASW][hapmap];0.87[GIH][hapmap]
rs7847	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7967503	0.86[ASN][1000 genomes]
rs7968763	0.81[JPT][hapmap]
rs7980681	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903247	0.94[CEU][hapmap];0.80[GIH][hapmap]
rs9669207	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2453166	CHST11	Cis_1M	lymphoblastoid	RTeQTL
rs2453166	C12orf23	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105187400-105213600	Weak transcription	Pancreas	Pancrea
2	chr12:105189800-105213400	Weak transcription	Aorta	Aorta
3	chr12:105197600-105218400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:105199200-105209800	Weak transcription	HSMMtube	muscle
5	chr12:105199600-105210400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:105199800-105218800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:105201200-105218200	Weak transcription	Gastric	stomach
8	chr12:105201400-105220600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:105201600-105210400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:105202800-105203800	Enhancers	HMEC	breast
11	chr12:105202800-105206600	Strong transcription	Liver	Liver
12	chr12:105203000-105203600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:105203000-105203800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:105203400-105203800	Enhancers	Thymus	Thymus
15	chr12:105203400-105204600	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links