Variant report

Variant	rs2270781
Chromosome Location	chr3:113015660-113015661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10934229	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs10934230	0.85[EUR][1000 genomes]
rs11710894	0.91[JPT][hapmap]
rs11717833	0.91[JPT][hapmap]
rs12630518	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs12634060	0.90[ASN][1000 genomes]
rs12634440	0.85[ASN][1000 genomes]
rs12635786	0.82[MEX][hapmap]
rs12636959	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637924	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12638030	0.81[JPT][hapmap]
rs13318454	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463644	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs16860850	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16860868	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16860899	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17882622	0.94[ASN][1000 genomes]
rs2291413	0.94[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap]
rs28662393	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34965320	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3814398	0.82[JPT][hapmap]
rs3846046	0.91[JPT][hapmap]
rs3856718	0.91[JPT][hapmap]
rs3856720	0.91[JPT][hapmap]
rs4682133	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682137	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs4682481	0.83[JPT][hapmap]
rs4682485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55667700	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55748551	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55757335	0.85[EUR][1000 genomes]
rs55973292	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438138	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438142	0.89[ASN][1000 genomes]
rs6801184	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809516	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73235059	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73235065	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73235066	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73235068	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73237104	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73237110	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73237123	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73237130	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73237143	0.85[EUR][1000 genomes]
rs73239107	0.85[EUR][1000 genomes]
rs73239126	0.81[EUR][1000 genomes]
rs763805	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs775222	0.81[JPT][hapmap]
rs8179926	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9820386	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]
rs9822309	0.94[ASN][1000 genomes]
rs9842039	0.91[ASN][1000 genomes]
rs9844111	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9847084	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9852204	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9857414	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9863193	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9878805	0.80[AMR][1000 genomes];0.94[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	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	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	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
rs2270781	WDR52	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
4	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
7	chr3:112995400-113035800	Weak transcription	Lung	lung
8	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
9	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
10	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
13	chr3:112998600-113036000	Weak transcription	Gastric	stomach
14	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
17	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
18	chr3:113003800-113016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:113004600-113016200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
23	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
24	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
25	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
26	chr3:113006800-113015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:113006800-113022600	Weak transcription	Hela-S3	cervix
28	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:113007000-113016400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:113007000-113022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:113007000-113022600	Weak transcription	Liver	Liver
32	chr3:113007000-113022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:113007000-113034400	Weak transcription	HSMM	muscle
36	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:113008000-113023600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
40	chr3:113008400-113023800	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:113008800-113016000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:113008800-113016000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:113009000-113032800	Weak transcription	Primary B cells from cord blood	blood
44	chr3:113010800-113022000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:113010800-113022600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:113010800-113031000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:113010800-113031400	Weak transcription	Fetal Stomach	stomach
48	chr3:113010800-113034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:113010800-113034400	Weak transcription	Fetal Lung	lung
50	chr3:113010800-113035800	Weak transcription	Ovary	ovary

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