Variant report

Variant	rs9820386
Chromosome Location	chr3:113095312-113095313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10934229	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934230	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934233	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10934234	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11710894	0.83[JPT][hapmap]
rs11717833	0.83[JPT][hapmap]
rs12630518	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12634060	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634440	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636959	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637924	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13318454	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1353903	0.84[MEX][hapmap];0.80[TSI][hapmap]
rs1392284	0.84[MEX][hapmap];0.80[TSI][hapmap]
rs1463640	0.80[TSI][hapmap]
rs1463644	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs16860850	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16860868	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16860899	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17882622	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270781	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs2291413	0.80[CHD][hapmap];0.82[MEX][hapmap]
rs2399481	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs28662393	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34965320	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846046	0.82[JPT][hapmap]
rs3856718	0.83[JPT][hapmap]
rs3856720	0.83[JPT][hapmap]
rs4682133	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682137	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4682485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55667700	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55748551	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55757335	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55973292	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438138	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438142	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801184	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6809516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235041	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73235059	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73235065	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73235066	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235068	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235093	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73237104	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73237110	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73237123	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73237130	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73237143	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73239107	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs763805	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8179926	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9810059	0.83[LWK][hapmap]
rs9822309	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9842039	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9844111	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9847084	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9852204	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863193	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9878805	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9820386	WDR52	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:113045400-113097600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:113066200-113102800	Weak transcription	Aorta	Aorta
5	chr3:113066400-113099000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:113066400-113117600	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:113068400-113117000	Weak transcription	Thymus	Thymus
8	chr3:113069000-113101800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:113070600-113099000	Weak transcription	Adipose Nuclei	Adipose
10	chr3:113072200-113096800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:113072400-113117200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
13	chr3:113077800-113102400	Weak transcription	HSMM	muscle
14	chr3:113078600-113109800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:113080000-113114200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:113080200-113117600	Weak transcription	Psoas Muscle	Psoas
18	chr3:113080800-113143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:113081600-113096800	Weak transcription	Primary T cells from cord blood	blood
20	chr3:113081600-113099000	Weak transcription	Left Ventricle	heart
21	chr3:113081600-113103400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:113081600-113104400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:113081600-113105600	Weak transcription	Esophagus	oesophagus
24	chr3:113081600-113105800	Weak transcription	Gastric	stomach
25	chr3:113081600-113106200	Weak transcription	Lung	lung
26	chr3:113081600-113121200	Weak transcription	Ovary	ovary
27	chr3:113081600-113121200	Weak transcription	Pancreas	Pancrea
28	chr3:113081800-113099000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:113081800-113116600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:113082200-113113200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:113086200-113105800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:113086200-113106400	Weak transcription	Fetal Stomach	stomach
33	chr3:113090800-113106600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:113090800-113121200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:113091800-113104600	Weak transcription	NH-A	brain
36	chr3:113092400-113134200	Weak transcription	Fetal Kidney	kidney
37	chr3:113093000-113098400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:113093000-113099400	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:113093600-113134800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:113094000-113095600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:113094200-113108800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:113094400-113096200	Strong transcription	Primary hematopoietic stem cells	blood

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