Variant report

Variant	rs2468090
Chromosome Location	chr12:105202665-105202666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1002803	0.82[EUR][1000 genomes]
rs1038968	0.82[EUR][1000 genomes]
rs1155994	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316594	0.88[EUR][1000 genomes]
rs1389609	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1389612	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565813	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1565815	0.87[EUR][1000 genomes]
rs2047124	0.82[EUR][1000 genomes]
rs2141248	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2245927	0.88[EUR][1000 genomes]
rs2245931	0.88[EUR][1000 genomes]
rs2248012	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2453157	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453158	0.90[EUR][1000 genomes]
rs2453160	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2453166	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2453167	0.88[EUR][1000 genomes]
rs2453168	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463016	0.88[EUR][1000 genomes]
rs2463017	0.88[EUR][1000 genomes]
rs2463018	0.83[EUR][1000 genomes]
rs2463025	0.88[EUR][1000 genomes]
rs2463429	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2463431	0.82[EUR][1000 genomes]
rs2463432	0.87[EUR][1000 genomes]
rs2463433	0.88[EUR][1000 genomes]
rs2468083	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468089	0.92[EUR][1000 genomes]
rs2468092	0.92[ASN][1000 genomes]
rs2468099	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468100	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468105	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468340	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2565167	0.88[EUR][1000 genomes]
rs2642110	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2642116	0.88[EUR][1000 genomes]
rs2730291	0.81[EUR][1000 genomes]
rs2730295	0.83[EUR][1000 genomes]
rs2731030	0.83[EUR][1000 genomes]
rs6539167	0.82[EUR][1000 genomes]
rs6539170	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847	0.83[EUR][1000 genomes]
rs7980681	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2468090	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 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	chr12:105190000-105202800	Weak transcription	Liver	Liver
4	chr12:105197600-105218400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:105199200-105209800	Weak transcription	HSMMtube	muscle
6	chr12:105199400-105202800	Weak transcription	NHEK	skin
7	chr12:105199400-105203000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:105199600-105202800	Weak transcription	HMEC	breast
9	chr12:105199600-105203000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:105199600-105210400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:105199800-105218800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:105201200-105218200	Weak transcription	Gastric	stomach
13	chr12:105201400-105220600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:105201600-105210400	Weak transcription	Duodenum Mucosa	Duodenum

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