Variant report

Variant	rs56002041
Chromosome Location	chr3:52409421-52409422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52384981..52388271-chr3:52408939..52411277,3	K562	blood:
2	chr3:52399836..52402473-chr3:52409418..52411150,2	K562	blood:
3	chr3:52378872..52380816-chr3:52409313..52412087,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10460962	0.97[EUR][1000 genomes]
rs10461027	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.91[EUR][1000 genomes]
rs10865971	0.88[EUR][1000 genomes]
rs11706515	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706541	0.87[EUR][1000 genomes]
rs11707056	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708581	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708811	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710014	0.97[EUR][1000 genomes]
rs11711914	0.88[EUR][1000 genomes]
rs11711974	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713914	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714358	0.94[EUR][1000 genomes]
rs11715208	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11715382	0.86[EUR][1000 genomes]
rs11715391	0.91[EUR][1000 genomes]
rs11716487	0.83[EUR][1000 genomes]
rs11717028	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.90[EUR][1000 genomes]
rs11719760	0.87[EUR][1000 genomes]
rs11720365	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11721277	1.00[EUR][1000 genomes]
rs17052051	0.90[EUR][1000 genomes]
rs17052052	0.93[EUR][1000 genomes]
rs17052053	0.90[EUR][1000 genomes]
rs17052054	0.94[EUR][1000 genomes]
rs17263770	0.87[EUR][1000 genomes]
rs1767	0.90[EUR][1000 genomes]
rs1769	0.94[EUR][1000 genomes]
rs35976326	0.94[EUR][1000 genomes]
rs3733063	0.90[EUR][1000 genomes]
rs3886875	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4082828	0.90[EUR][1000 genomes]
rs55676974	0.94[EUR][1000 genomes]
rs55724529	1.00[AFR][1000 genomes]
rs55806905	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55813842	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55847657	0.90[EUR][1000 genomes]
rs55946513	1.00[AFR][1000 genomes]
rs56322342	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56352611	0.90[EUR][1000 genomes]
rs56366004	1.00[AFR][1000 genomes]
rs56899118	1.00[EUR][1000 genomes]
rs57849650	0.83[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	0.96[EUR][1000 genomes]
rs6776759	0.87[EUR][1000 genomes]
rs6783652	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	0.93[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	0.94[EUR][1000 genomes]
rs73088800	0.90[EUR][1000 genomes]
rs73088802	1.00[AFR][1000 genomes]
rs73091166	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091168	1.00[EUR][1000 genomes]
rs746239	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615405	0.97[EUR][1000 genomes]
rs7628461	0.90[EUR][1000 genomes]
rs7633687	0.93[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: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	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
5	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
4	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
6	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
7	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
9	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
11	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:52407200-52413800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52407200-52422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:52407600-52412400	Weak transcription	Thymus	Thymus
16	chr3:52407600-52413800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:52407600-52420800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:52407800-52421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:52408000-52409600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52408000-52412000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:52408000-52419200	Weak transcription	Fetal Thymus	thymus
22	chr3:52408000-52421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
25	chr3:52408600-52411200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:52408600-52421000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:52408800-52414000	Weak transcription	K562	blood
28	chr3:52409000-52410400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:52409000-52411000	Strong transcription	Primary T cells from cord blood	blood
30	chr3:52409000-52411000	Strong transcription	Liver	Liver
31	chr3:52409200-52409600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:52409200-52409800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr3:52409200-52410000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:52409200-52410200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr3:52409200-52410400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:52409200-52410400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:52409200-52410400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:52409200-52410400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:52409200-52410600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:52409200-52410600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:52409200-52410600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:52409200-52410600	Strong transcription	Brain Substantia Nigra	brain
43	chr3:52409200-52410600	Strong transcription	Fetal Intestine Large	intestine
44	chr3:52409200-52410600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:52409200-52410800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:52409200-52410800	Strong transcription	Spleen	Spleen
47	chr3:52409200-52411000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:52409200-52411000	Strong transcription	Lung	lung
49	chr3:52409200-52411000	Strong transcription	Pancreas	Pancrea
50	chr3:52409200-52411400	Strong transcription	Placenta	Placenta

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