Variant report

Variant	rs1565813
Chromosome Location	chr12:105253927-105253928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105252367..105254848-chr12:105257753..105259443,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1002803	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10507184	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1070316	0.86[JPT][hapmap]
rs10746008	0.81[JPT][hapmap]
rs10778358	0.86[ASW][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs1155994	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1316594	0.87[EUR][1000 genomes]
rs1389609	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1389612	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474459	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs1565815	0.86[EUR][1000 genomes]
rs2047124	0.80[EUR][1000 genomes]
rs2131806	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs2141248	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2245927	0.87[EUR][1000 genomes]
rs2245931	0.87[EUR][1000 genomes]
rs2248012	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249454	0.86[ASW][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs2453154	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs2453155	0.88[CEU][hapmap];0.89[GIH][hapmap]
rs2453156	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs2453157	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2453158	0.87[EUR][1000 genomes]
rs2453160	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453161	0.83[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2453166	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]
rs2453167	0.87[EUR][1000 genomes]
rs2453168	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2463016	0.87[EUR][1000 genomes]
rs2463017	0.87[EUR][1000 genomes]
rs2463018	0.83[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs2463025	0.87[EUR][1000 genomes]
rs2463429	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463431	0.80[EUR][1000 genomes]
rs2463432	0.86[EUR][1000 genomes]
rs2463433	0.87[EUR][1000 genomes]
rs2463437	0.88[CEU][hapmap];0.84[GIH][hapmap]
rs2463438	0.88[CEU][hapmap]
rs2463439	0.88[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2463440	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs2463441	0.83[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2468083	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2468089	0.94[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs2468090	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2468092	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2468099	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468100	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468105	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468109	0.83[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2468110	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs2468340	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2565167	0.87[EUR][1000 genomes]
rs2642110	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2642116	0.87[EUR][1000 genomes]
rs2730291	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap]
rs2730295	0.81[EUR][1000 genomes]
rs2731030	0.81[EUR][1000 genomes]
rs4334113	0.81[ASN][1000 genomes]
rs4388976	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4393404	0.86[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6539167	0.80[EUR][1000 genomes]
rs6539170	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6539171	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs703681	0.83[CEU][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs7135015	0.86[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs7138686	0.86[ASW][hapmap];0.89[GIH][hapmap]
rs7847	0.82[EUR][1000 genomes]
rs7968763	0.81[JPT][hapmap]
rs7980681	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs903247	0.88[CEU][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs1565813	C12orf23	cis	parietal	SCAN
rs1565813	CHST11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105220800-105260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105222000-105258400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:105222000-105258600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:105222200-105258800	Weak transcription	Pancreas	Pancrea
5	chr12:105229000-105259200	Weak transcription	Placenta	Placenta
6	chr12:105233200-105258600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:105236200-105258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:105237400-105259000	Weak transcription	A549	lung
9	chr12:105238400-105257000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:105238400-105260400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:105238400-105280000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:105240600-105258800	Weak transcription	Aorta	Aorta
13	chr12:105243000-105255800	Weak transcription	Colonic Mucosa	Colon
14	chr12:105243800-105265800	Weak transcription	Fetal Stomach	stomach
15	chr12:105248000-105269000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:105248800-105259600	Strong transcription	Liver	Liver
17	chr12:105251400-105257000	Weak transcription	Left Ventricle	heart
18	chr12:105252200-105259000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:105252400-105254000	Enhancers	Brain Germinal Matrix	brain
20	chr12:105253400-105257000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:105253400-105257000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:105253400-105257000	Weak transcription	HSMMtube	muscle
23	chr12:105253400-105257000	Weak transcription	NH-A	brain
24	chr12:105253400-105257000	Weak transcription	NHLF	lung
25	chr12:105253400-105257000	Weak transcription	Osteobl	bone
26	chr12:105253400-105257600	Weak transcription	Hela-S3	cervix
27	chr12:105253600-105255800	Weak transcription	NHDF-Ad	bronchial
28	chr12:105253600-105257000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:105253800-105257000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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