Variant report

Variant	rs1463644
Chromosome Location	chr3:113197393-113197394
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10934229	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934230	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12054036	0.93[EUR][1000 genomes]
rs12629271	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629498	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12630518	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632492	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637924	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16860850	0.81[EUR][1000 genomes]
rs16860868	0.81[EUR][1000 genomes]
rs16860899	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2270781	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs2271495	0.84[TSI][hapmap]
rs2291413	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[MEX][hapmap]
rs2306069	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2399481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732804	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682137	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682485	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs4682489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55667700	0.81[EUR][1000 genomes]
rs55748551	0.81[EUR][1000 genomes]
rs55757335	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55865352	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60292736	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62265992	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62265996	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6809516	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs73235059	0.80[EUR][1000 genomes]
rs73235065	0.81[EUR][1000 genomes]
rs73237104	0.86[EUR][1000 genomes]
rs73237110	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73237123	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73237130	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73237143	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73239107	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73239126	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643592	0.87[CHB][hapmap]
rs7643843	0.87[CHB][hapmap]
rs7647220	0.83[CHB][hapmap]
rs7653186	0.87[CHB][hapmap]
rs8179926	0.86[EUR][1000 genomes]
rs9820386	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs9857414	0.91[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3338413	chr3:113194262-113198760	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	esv3371337	chr3:113195862-113200260	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1463644	WDR52	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113160600-113203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:113160800-113203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:113160800-113203800	Weak transcription	Aorta	Aorta
4	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
5	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
6	chr3:113166600-113203800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:113172600-113203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
9	chr3:113176400-113233200	Weak transcription	Gastric	stomach
10	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
12	chr3:113179600-113204000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:113179600-113215200	Weak transcription	HMEC	breast
14	chr3:113179600-113217200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:113179600-113232400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:113179600-113232800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:113182000-113203800	Weak transcription	Esophagus	oesophagus
18	chr3:113182000-113203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
20	chr3:113184800-113204800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:113187200-113203800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:113187200-113203800	Weak transcription	Ovary	ovary
23	chr3:113187200-113207200	Weak transcription	Thymus	Thymus
24	chr3:113187200-113224400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:113187400-113203800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:113187400-113203800	Weak transcription	Hela-S3	cervix
27	chr3:113187800-113203800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:113187800-113203800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:113187800-113203800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:113187800-113204600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:113187800-113207000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:113187800-113209400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:113188000-113203800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:113188000-113203800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:113188000-113203800	Weak transcription	Dnd41	blood
36	chr3:113188000-113206000	Weak transcription	Liver	Liver
37	chr3:113188000-113206200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:113188000-113207000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:113188000-113211400	Weak transcription	Osteobl	bone
40	chr3:113188000-113215000	Weak transcription	NH-A	brain
41	chr3:113188200-113203800	Weak transcription	Left Ventricle	heart
42	chr3:113189000-113203800	Weak transcription	Fetal Lung	lung
43	chr3:113189000-113203800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:113189000-113206000	Weak transcription	Adipose Nuclei	Adipose
45	chr3:113189000-113207200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:113189200-113207000	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:113189400-113203800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:113189800-113203800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:113189800-113203800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:113189800-113208000	Weak transcription	Fetal Kidney	kidney

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