Variant report

Variant	rs2270783
Chromosome Location	chr3:113023675-113023676
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:113023653-113024028	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
WDR52	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1082588	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1082589	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330209	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12330211	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082603	0.85[CEU][hapmap]
rs1471883	0.89[CEU][hapmap]
rs1471884	0.90[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs2270782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291905	0.81[GIH][hapmap];0.93[TSI][hapmap]
rs2399477	0.85[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap]
rs2936812	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4396864	0.89[CEU][hapmap]
rs6438137	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769604	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs6783479	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793192	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801402	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712530	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618847	0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7623919	0.89[CEU][hapmap]
rs7637618	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs7646188	0.90[CEU][hapmap]
rs775214	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775215	0.95[CEU][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs775217	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808949	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808950	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs810209	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852703	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2270783	BOC	cis	cerebellum	SCAN
rs2270783	BOC	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
3	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
4	chr3:112995400-113035800	Weak transcription	Lung	lung
5	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
6	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
7	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
10	chr3:112998600-113036000	Weak transcription	Gastric	stomach
11	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
13	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
15	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
16	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
17	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
18	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:113007000-113034400	Weak transcription	HSMM	muscle
22	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:113008400-113023800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:113009000-113032800	Weak transcription	Primary B cells from cord blood	blood
27	chr3:113010800-113031000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:113010800-113031400	Weak transcription	Fetal Stomach	stomach
29	chr3:113010800-113034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:113010800-113034400	Weak transcription	Fetal Lung	lung
31	chr3:113010800-113035800	Weak transcription	Ovary	ovary
32	chr3:113011000-113036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:113011600-113034000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:113013600-113034400	Weak transcription	A549	lung
35	chr3:113013600-113065200	Weak transcription	Left Ventricle	heart
36	chr3:113015400-113031400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:113017200-113032600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:113017800-113036000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:113018800-113031800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:113019200-113024200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:113020200-113032400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:113020800-113026000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:113020800-113041200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:113021200-113029600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:113022000-113023800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:113022000-113024600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:113022000-113025200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:113022400-113025600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:113022600-113023800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:113022600-113024000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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