Variant report

Variant	rs2270784
Chromosome Location	chr3:113024002-113024003
allele	A/G
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	chr3:113023860-113024010	HAc	cerebellar:	n/a	n/a
2	CTCF	chr3:113023727-113024055	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr3:113023708-113024034	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:113023653-113024028	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAL1	chr3:113023776-113024057	K562	blood:	n/a	n/a
6	BRCA1	chr3:113023876-113024009	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:113023860-113024010	HEK293	kidney:	n/a	n/a
8	POLR2A	chr3:113023708-113024185	H1-neurons	neurons:	n/a	n/a
9	RAD21	chr3:113023712-113024065	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
WDR52	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs2306792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57006145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57251392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57357573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57414437	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57417572	1.00[ASN][1000 genomes]
rs57591967	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57797139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58121831	1.00[ASN][1000 genomes]
rs58248101	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58551767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58890779	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58992191	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59275119	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59911537	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60874642	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61151383	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61258912	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6768642	1.00[ASN][1000 genomes]
rs6780086	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6790910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs7619717	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7621031	1.00[ASN][1000 genomes]
rs7621039	1.00[ASN][1000 genomes]
rs7622062	1.00[ASN][1000 genomes]
rs775218	1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[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
rs2270784	CCDC52	cis	multi-tissue	Pritchard

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	chr3:112995400-113035800	Weak transcription	Lung	lung
4	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
5	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
6	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
9	chr3:112998600-113036000	Weak transcription	Gastric	stomach
10	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
12	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
14	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
15	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:113007000-113034400	Weak transcription	HSMM	muscle
18	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
21	chr3:113009000-113032800	Weak transcription	Primary B cells from cord blood	blood
22	chr3:113010800-113031000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:113010800-113031400	Weak transcription	Fetal Stomach	stomach
24	chr3:113010800-113034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:113010800-113034400	Weak transcription	Fetal Lung	lung
26	chr3:113010800-113035800	Weak transcription	Ovary	ovary
27	chr3:113011000-113036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:113011600-113034000	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:113013600-113034400	Weak transcription	A549	lung
30	chr3:113013600-113065200	Weak transcription	Left Ventricle	heart
31	chr3:113015400-113031400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:113017200-113032600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:113017800-113036000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:113018800-113031800	Weak transcription	Adipose Nuclei	Adipose
35	chr3:113019200-113024200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:113020200-113032400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:113020800-113026000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:113020800-113041200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:113021200-113029600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:113022000-113024600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:113022000-113025200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:113022400-113025600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr3:113022600-113024600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:113022600-113025600	Strong transcription	Liver	Liver
45	chr3:113022600-113035800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:113023000-113030600	Weak transcription	Primary T cells from cord blood	blood
47	chr3:113023200-113034000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:113023200-113034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:113023200-113034400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:113023400-113028400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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