Variant report

Variant	rs56653941
Chromosome Location	chr3:69417532-69417533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69416233..69418620-chr3:69433830..69435946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13320477	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17005675	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17005685	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17005687	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005689	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005691	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005694	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005696	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416638	0.81[AMR][1000 genomes]
rs2314987	0.89[AMR][1000 genomes]
rs2872808	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4241387	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5026329	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56682655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58937767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59683429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60969945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940765	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940769	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940771	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940775	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940779	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940783	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940785	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881031	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs964553	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2760780	chr3:69413876-69513947	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:69413600-69417600	Weak transcription	Esophagus	oesophagus
3	chr3:69413600-69418000	Weak transcription	HSMMtube	muscle
4	chr3:69413600-69419000	Weak transcription	NHDF-Ad	bronchial
5	chr3:69413800-69417600	Weak transcription	Placenta	Placenta
6	chr3:69413800-69417600	Weak transcription	Right Atrium	heart
7	chr3:69413800-69419000	Weak transcription	Brain Angular Gyrus	brain
8	chr3:69413800-69419400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:69414000-69418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:69414000-69419000	Weak transcription	Osteobl	bone
11	chr3:69414200-69418000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:69415000-69418800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:69416000-69419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:69416000-69419200	Weak transcription	Fetal Brain Male	brain
15	chr3:69416600-69418400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:69416600-69420400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:69416800-69419800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:69416800-69420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:69416800-69420600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:69417000-69417600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:69417000-69417800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr3:69417000-69419000	Enhancers	HUVEC	blood vessel
23	chr3:69417000-69419200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:69417000-69419400	Enhancers	Primary B cells from cord blood	blood
25	chr3:69417000-69420600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:69417000-69420600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:69417200-69417600	Enhancers	Thymus	Thymus
28	chr3:69417200-69417800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:69417200-69417800	Enhancers	Aorta	Aorta
30	chr3:69417200-69417800	Enhancers	Spleen	Spleen
31	chr3:69417200-69418000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:69417200-69418000	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:69417200-69418200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr3:69417200-69418200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:69417200-69418400	Enhancers	Primary B cells from peripheral blood	blood
36	chr3:69417200-69418400	Enhancers	Fetal Thymus	thymus
37	chr3:69417200-69419000	Enhancers	HMEC	breast
38	chr3:69417200-69419000	Enhancers	NHEK	skin
39	chr3:69417200-69419400	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:69417200-69419400	Enhancers	Brain Hippocampus Middle	brain
41	chr3:69417200-69419400	Enhancers	HSMM	muscle
42	chr3:69417200-69420600	Flanking Active TSS	Dnd41	blood
43	chr3:69417200-69421000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:69417400-69417600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:69417400-69417800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:69417400-69417800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr3:69417400-69417800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr3:69417400-69417800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:69417400-69417800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:69417400-69417800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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