Variant report

Variant	rs3752819
Chromosome Location	chr3:52400740-52400741
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52399836..52402473-chr3:52409418..52411150,2	K562	blood:
2	chr3:52393060..52394976-chr3:52400289..52402060,2	K562	blood:
3	chr3:52269274..52272214-chr3:52398381..52400803,2	K562	blood:
4	chr3:52399471..52401376-chr3:52402846..52405775,2	K562	blood:
5	chr3:52272785..52274922-chr3:52398332..52400991,2	K562	blood:

Variant related genes	Relation type
ENSG00000247596	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1077142	0.92[EUR][1000 genomes]
rs11705963	0.92[EUR][1000 genomes]
rs11706001	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706108	0.92[EUR][1000 genomes]
rs11707864	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707931	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711934	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11711974	0.82[AFR][1000 genomes]
rs11714402	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11716017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718125	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11721277	0.83[AFR][1000 genomes]
rs123598	1.00[ASN][1000 genomes]
rs123602	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs123603	1.00[ASN][1000 genomes]
rs13059674	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13060192	1.00[ASN][1000 genomes]
rs13075370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076508	1.00[ASN][1000 genomes]
rs13076890	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13089892	1.00[ASN][1000 genomes]
rs13091360	1.00[ASN][1000 genomes]
rs13091545	0.93[EUR][1000 genomes]
rs13096571	1.00[ASN][1000 genomes]
rs17052058	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052061	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052068	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016575	0.86[EUR][1000 genomes]
rs2109557	1.00[ASN][1000 genomes]
rs2335640	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28481563	0.92[EUR][1000 genomes]
rs2878549	1.00[ASN][1000 genomes]
rs34181173	1.00[ASN][1000 genomes]
rs34238085	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34261027	0.80[EUR][1000 genomes]
rs34332947	1.00[ASN][1000 genomes]
rs34355561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523877	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34628357	1.00[ASN][1000 genomes]
rs34762015	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34827613	1.00[ASN][1000 genomes]
rs34908451	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133416	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860312	0.92[EUR][1000 genomes]
rs35982798	1.00[ASN][1000 genomes]
rs3796343	0.84[EUR][1000 genomes]
rs390802	0.94[EUR][1000 genomes]
rs419050	1.00[ASN][1000 genomes]
rs419604	1.00[ASN][1000 genomes]
rs419752	1.00[ASN][1000 genomes]
rs498778	1.00[ASN][1000 genomes]
rs498946	0.90[EUR][1000 genomes]
rs55965068	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55997317	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.82[AFR][1000 genomes]
rs56357549	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.87[AFR][1000 genomes]
rs57441156	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs575476	1.00[ASN][1000 genomes]
rs59612757	0.91[EUR][1000 genomes]
rs61150019	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61734640	1.00[ASN][1000 genomes]
rs634382	0.80[EUR][1000 genomes]
rs6445386	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66462821	0.93[EUR][1000 genomes]
rs67248391	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67834575	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794675	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795333	1.00[ASN][1000 genomes]
rs6796333	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6800707	0.83[EUR][1000 genomes]
rs71297391	1.00[ASN][1000 genomes]
rs71297394	1.00[ASN][1000 genomes]
rs71297395	1.00[ASN][1000 genomes]
rs71297396	1.00[ASN][1000 genomes]
rs73091168	0.87[AFR][1000 genomes]
rs7643570	0.93[EUR][1000 genomes]
rs82825	0.89[EUR][1000 genomes]
rs9844183	0.90[EUR][1000 genomes]
rs9861879	0.92[EUR][1000 genomes]

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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv979833	chr3:52387550-52407592	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
2	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:52375400-52405600	Strong transcription	Lung	lung
4	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:52377000-52406600	Strong transcription	Liver	Liver
7	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
14	chr3:52378400-52401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:52378400-52401200	Strong transcription	Gastric	stomach
16	chr3:52378400-52401800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:52380400-52401000	Strong transcription	Placenta	Placenta
21	chr3:52381400-52401200	Strong transcription	Ovary	ovary
22	chr3:52381400-52402600	Strong transcription	Fetal Stomach	stomach
23	chr3:52381400-52404200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:52381400-52407400	Weak transcription	NHLF	lung
25	chr3:52381600-52405400	Strong transcription	Adipose Nuclei	Adipose
26	chr3:52381600-52405800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:52383000-52401400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:52384600-52406200	Weak transcription	GM12878-XiMat	blood
29	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
30	chr3:52386000-52406600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:52387600-52402200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:52388600-52403400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:52390400-52403200	Strong transcription	Spleen	Spleen
34	chr3:52390400-52405600	Weak transcription	Fetal Brain Female	brain
35	chr3:52391400-52401000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr3:52391600-52401400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:52392200-52406400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:52392400-52401000	Strong transcription	Esophagus	oesophagus
39	chr3:52392400-52401200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:52392600-52406600	Strong transcription	Primary T cells from cord blood	blood
41	chr3:52393000-52406400	Strong transcription	Thymus	Thymus
42	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:52393600-52404600	Strong transcription	Primary B cells from cord blood	blood
44	chr3:52395000-52401400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
46	chr3:52395200-52407200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
49	chr3:52396000-52404200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:52396200-52402200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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