Variant report

Variant	rs56161503
Chromosome Location	chr2:46615955-46615956
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	chr2:46300290..46302585-chr2:46613885..46616357,2	MCF-7	breast:
2	chr2:46609393..46611243-chr2:46614056..46616065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171132	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11675232	0.90[AMR][1000 genomes]
rs11675328	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11675441	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11678465	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11678817	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11681242	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11686705	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11689649	0.82[EUR][1000 genomes]
rs11689694	0.82[EUR][1000 genomes]
rs11690951	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11691694	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11692911	0.85[AMR][1000 genomes]
rs11693596	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11693754	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11694193	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13006131	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1530622	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1868092	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55826825	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59034065	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62138871	0.92[AMR][1000 genomes]
rs7557402	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7567582	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7583088	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7583392	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7591548	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7594278	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7598371	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7606559	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
2	chr2:46592200-46619800	Weak transcription	K562	blood
3	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr2:46595000-46616000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:46601800-46616400	Genic enhancers	Placenta	Placenta
6	chr2:46602000-46616000	Strong transcription	Pancreas	Pancrea
7	chr2:46607000-46617000	Weak transcription	Stomach Mucosa	stomach
8	chr2:46609000-46617000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:46611200-46616800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:46611600-46616600	Weak transcription	Fetal Intestine Large	intestine
11	chr2:46612000-46616800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:46612000-46620600	Weak transcription	Psoas Muscle	Psoas
13	chr2:46612000-46622400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:46612600-46617000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:46612800-46616600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:46613200-46616600	Weak transcription	Ovary	ovary
17	chr2:46613200-46644200	Weak transcription	Aorta	Aorta
18	chr2:46613400-46616200	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:46613400-46616600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:46613400-46616600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:46613400-46616600	Weak transcription	Gastric	stomach
22	chr2:46613400-46616800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:46613400-46617200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:46613400-46617400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:46613400-46617400	Weak transcription	Colonic Mucosa	Colon
26	chr2:46613600-46616800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:46613800-46616000	Strong transcription	NHLF	lung
28	chr2:46614000-46616000	Weak transcription	NHDF-Ad	bronchial
29	chr2:46614000-46617200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:46614200-46616400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:46614200-46616400	Enhancers	Brain Substantia Nigra	brain
32	chr2:46614200-46616800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:46614400-46616200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:46614400-46616200	Enhancers	Right Atrium	heart
35	chr2:46614400-46616400	Enhancers	Brain Angular Gyrus	brain
36	chr2:46614400-46616400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr2:46614400-46617200	Enhancers	Brain Hippocampus Middle	brain
38	chr2:46614400-46620600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:46614600-46616200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:46614600-46616400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:46614600-46617600	Enhancers	HepG2	liver
42	chr2:46614600-46623000	Weak transcription	Esophagus	oesophagus
43	chr2:46615200-46616800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr2:46615400-46616000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:46615400-46616000	Weak transcription	Hela-S3	cervix
46	chr2:46615400-46616200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:46615400-46624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:46615600-46616800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr2:46615600-46617200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:46615600-46617400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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