Variant report

Variant	rs55813842
Chromosome Location	chr3:52367172-52367173
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52361577..52363377-chr3:52366056..52367676,2	K562	blood:
2	chr3:52350198..52352683-chr3:52366268..52368168,2	K562	blood:
3	chr3:52310953..52312726-chr3:52365958..52368277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10460962	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461027	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.91[EUR][1000 genomes]
rs10865971	0.88[EUR][1000 genomes]
rs11706515	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706541	0.87[EUR][1000 genomes]
rs11707056	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708581	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708811	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710014	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711914	0.88[EUR][1000 genomes]
rs11711974	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713914	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714358	0.94[EUR][1000 genomes]
rs11715208	0.94[EUR][1000 genomes]
rs11715382	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11715391	0.91[EUR][1000 genomes]
rs11716487	0.83[EUR][1000 genomes]
rs11717028	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.90[EUR][1000 genomes]
rs11719760	0.87[EUR][1000 genomes]
rs11720365	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11721277	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052051	0.90[EUR][1000 genomes]
rs17052052	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052053	0.90[EUR][1000 genomes]
rs17052054	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17263770	0.87[EUR][1000 genomes]
rs1767	0.90[EUR][1000 genomes]
rs1769	0.94[EUR][1000 genomes]
rs35976326	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3733063	0.90[EUR][1000 genomes]
rs3886875	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4082828	0.90[EUR][1000 genomes]
rs55676974	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55806905	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55847657	0.90[EUR][1000 genomes]
rs56002041	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56322342	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56352611	0.90[EUR][1000 genomes]
rs56899118	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57849650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58531656	0.90[EUR][1000 genomes]
rs60382084	0.90[EUR][1000 genomes]
rs61644644	0.94[EUR][1000 genomes]
rs6445385	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776759	0.87[EUR][1000 genomes]
rs6783652	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6793317	0.90[EUR][1000 genomes]
rs6809248	0.90[EUR][1000 genomes]
rs724801	0.88[EUR][1000 genomes]
rs729555	0.88[EUR][1000 genomes]
rs73072990	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088773	0.91[EUR][1000 genomes]
rs73088783	0.90[EUR][1000 genomes]
rs73088785	0.90[EUR][1000 genomes]
rs73088791	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088800	0.90[EUR][1000 genomes]
rs73091166	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091168	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs746239	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615405	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628461	0.90[EUR][1000 genomes]
rs7633687	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638204	0.91[EUR][1000 genomes]
rs7643913	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
3	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
4	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:52352000-52367600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:52352200-52370800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:52352200-52379000	Weak transcription	Colonic Mucosa	Colon
8	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:52352600-52373400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:52352600-52379400	Weak transcription	Pancreas	Pancrea
12	chr3:52353400-52377400	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
14	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:52358200-52372000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:52358400-52370200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:52358400-52380400	Weak transcription	Ovary	ovary
18	chr3:52360400-52376200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:52361000-52367800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:52361800-52368400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:52362200-52375000	Weak transcription	Fetal Thymus	thymus
22	chr3:52362400-52378200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:52362800-52378600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:52364200-52367800	Strong transcription	Fetal Stomach	stomach
25	chr3:52364200-52368600	Strong transcription	Primary T cells from cord blood	blood
26	chr3:52364200-52375800	Weak transcription	GM12878-XiMat	blood
27	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
28	chr3:52364400-52367800	Strong transcription	Fetal Intestine Small	intestine
29	chr3:52364400-52379400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:52364600-52367600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:52364600-52368800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:52364800-52368000	Weak transcription	Left Ventricle	heart
33	chr3:52364800-52368400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:52364800-52368600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:52364800-52373400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:52364800-52373400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
38	chr3:52365000-52367200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:52365000-52368800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:52365000-52368800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:52365000-52372200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:52365200-52367200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:52365200-52368000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:52365200-52368600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:52365200-52368800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:52365200-52368800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:52365200-52368800	Strong transcription	Liver	Liver
48	chr3:52365200-52368800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:52365200-52368800	Strong transcription	Placenta	Placenta
50	chr3:52365400-52368800	Strong transcription	Rectal Mucosa Donor 29	rectum

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