Variant report

Variant	rs2468089
Chromosome Location	chr12:105199544-105199545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];0.85[GIH][hapmap];0.86[EUR][1000 genomes]
rs1038968	0.85[EUR][1000 genomes]
rs10507184	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap]
rs1070316	0.82[CEU][hapmap]
rs10778358	0.82[GIH][hapmap]
rs1155994	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1316594	0.91[EUR][1000 genomes]
rs1389609	0.94[EUR][1000 genomes]
rs1389612	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1474459	0.89[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs1565813	0.94[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs1565815	0.90[EUR][1000 genomes]
rs2047124	0.86[EUR][1000 genomes]
rs2131806	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs2141248	0.89[EUR][1000 genomes]
rs2245927	0.91[EUR][1000 genomes]
rs2245931	0.91[EUR][1000 genomes]
rs2248012	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2249454	0.80[GIH][hapmap]
rs2453154	0.94[CEU][hapmap];0.89[GIH][hapmap]
rs2453155	0.94[CEU][hapmap];0.83[GIH][hapmap]
rs2453156	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2453157	0.93[EUR][1000 genomes]
rs2453158	0.93[EUR][1000 genomes]
rs2453160	0.96[EUR][1000 genomes]
rs2453161	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2453166	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]
rs2453167	0.91[EUR][1000 genomes]
rs2453168	0.94[EUR][1000 genomes]
rs2463016	0.91[EUR][1000 genomes]
rs2463017	0.91[EUR][1000 genomes]
rs2463018	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[EUR][1000 genomes]
rs2463025	0.91[EUR][1000 genomes]
rs2463429	0.94[EUR][1000 genomes]
rs2463431	0.85[EUR][1000 genomes]
rs2463432	0.90[EUR][1000 genomes]
rs2463433	0.91[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2463441	0.89[CEU][hapmap]
rs2463442	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs2463443	0.84[CEU][hapmap]
rs2463444	0.84[CEU][hapmap]
rs2468083	0.94[EUR][1000 genomes]
rs2468090	0.92[EUR][1000 genomes]
rs2468092	0.81[EUR][1000 genomes]
rs2468099	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2468100	0.95[EUR][1000 genomes]
rs2468105	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2468109	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2468110	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs2468112	0.81[EUR][1000 genomes]
rs2468340	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2565167	0.91[EUR][1000 genomes]
rs2642110	0.94[EUR][1000 genomes]
rs2642116	0.91[EUR][1000 genomes]
rs2730291	0.94[CEU][hapmap];0.85[GIH][hapmap];0.85[EUR][1000 genomes]
rs2730295	0.86[EUR][1000 genomes]
rs2731030	0.86[EUR][1000 genomes]
rs4393404	0.82[GIH][hapmap]
rs6539167	0.86[EUR][1000 genomes]
rs6539170	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs703681	0.89[CEU][hapmap]
rs7135015	0.82[GIH][hapmap]
rs7847	0.87[EUR][1000 genomes]
rs7980681	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs903247	0.94[CEU][hapmap];0.89[GIH][hapmap]

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
rs2468089	C12orf23	cis	parietal	SCAN
rs2468089	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 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	chr12:105198400-105199600	Enhancers	HSMM	muscle
6	chr12:105198400-105199600	Enhancers	NH-A	brain
7	chr12:105198600-105199600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:105198800-105199600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:105198800-105199600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:105198800-105199600	Enhancers	HMEC	breast
11	chr12:105199000-105199600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:105199200-105199800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:105199200-105209800	Weak transcription	HSMMtube	muscle
14	chr12:105199400-105199600	Enhancers	Osteobl	bone
15	chr12:105199400-105199800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:105199400-105202800	Weak transcription	NHEK	skin
17	chr12:105199400-105203000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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