Variant report

Variant	rs2468092
Chromosome Location	chr12:105207724-105207725
allele	A/G
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	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10507184	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1070316	0.81[JPT][hapmap]
rs10746008	0.80[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10778358	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1155994	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389609	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1389612	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565813	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2141248	0.87[ASN][1000 genomes]
rs2248012	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249454	0.81[JPT][hapmap]
rs2453156	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2453157	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2453160	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453161	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2453166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453168	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2463018	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2463429	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2463439	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2463440	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2463441	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2468083	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2468089	0.81[EUR][1000 genomes]
rs2468090	0.92[ASN][1000 genomes]
rs2468099	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468100	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468105	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468109	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2468340	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2642110	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730291	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4334113	0.85[ASN][1000 genomes]
rs4388976	0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs4393404	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6539170	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6539171	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs703681	0.93[JPT][hapmap]
rs7135015	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7967503	0.86[ASN][1000 genomes]
rs7968763	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7980681	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2468092	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 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	chr12:105205000-105213600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:105205000-105218400	Weak transcription	Fetal Stomach	stomach
12	chr12:105205400-105209000	Weak transcription	Stomach Mucosa	stomach
13	chr12:105205400-105217800	Weak transcription	Esophagus	oesophagus
14	chr12:105206600-105208800	Weak transcription	Liver	Liver
15	chr12:105206600-105217800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:105207600-105211200	Weak transcription	Lung	lung

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