Variant report

Variant	rs2456272
Chromosome Location	chr16:12252055-12252056
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12251094..12253122-chr16:12351083..12352799,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11642667	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1701111	0.89[AMR][1000 genomes]
rs1704094	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1704130	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968353	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs709418	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709419	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709420	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709421	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs709422	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8062913	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs830696	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830698	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830700	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830701	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830704	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs830705	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830706	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830707	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830708	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830709	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830710	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830724	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs830725	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs844224	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs844225	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853869	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853870	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862692	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs865533	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs866180	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs905952	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937965	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9934120	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr16:12231400-12268000	Weak transcription	Pancreas	Pancrea
5	chr16:12234600-12261600	Weak transcription	Aorta	Aorta
6	chr16:12234600-12265600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr16:12242200-12252400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr16:12242200-12252400	Weak transcription	Left Ventricle	heart
9	chr16:12242200-12252600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr16:12242200-12252600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr16:12242200-12253800	Weak transcription	Right Atrium	heart
12	chr16:12242200-12255200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:12242200-12261600	Weak transcription	Lung	lung
14	chr16:12242200-12262800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr16:12242400-12252400	Weak transcription	Right Ventricle	heart
17	chr16:12242400-12252600	Weak transcription	Fetal Brain Female	brain
18	chr16:12242400-12252800	Weak transcription	Brain Anterior Caudate	brain
19	chr16:12242400-12255800	Weak transcription	Thymus	Thymus
20	chr16:12242400-12256400	Weak transcription	Fetal Kidney	kidney
21	chr16:12242400-12264600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:12242400-12280600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr16:12243200-12255400	Weak transcription	Psoas Muscle	Psoas
24	chr16:12244000-12252800	Weak transcription	Fetal Muscle Leg	muscle
25	chr16:12244400-12255800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr16:12244800-12261200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:12245600-12257200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr16:12245600-12261800	Weak transcription	Fetal Thymus	thymus
29	chr16:12246600-12252400	Weak transcription	Brain Hippocampus Middle	brain
30	chr16:12247000-12252400	Weak transcription	Brain Substantia Nigra	brain
31	chr16:12247400-12259400	Strong transcription	Primary B cells from cord blood	blood
32	chr16:12248000-12258400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr16:12248200-12255200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr16:12248800-12254000	Strong transcription	Adipose Nuclei	Adipose
35	chr16:12248800-12257800	Strong transcription	Primary T cells from cord blood	blood
36	chr16:12249600-12254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr16:12249600-12256400	Weak transcription	HepG2	liver
38	chr16:12249800-12252200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr16:12250000-12257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr16:12250000-12260800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr16:12250600-12252800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr16:12250600-12253000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:12250600-12254000	Enhancers	HSMM	muscle
44	chr16:12250800-12252800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:12251000-12252400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr16:12251000-12252600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr16:12251000-12253200	Enhancers	NHDF-Ad	bronchial
48	chr16:12251000-12253400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:12251000-12253400	Weak transcription	Fetal Stomach	stomach
50	chr16:12251000-12255000	Enhancers	NH-A	brain

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