Variant report

Variant	rs16859392
Chromosome Location	chr2:172318148-172318149
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172317786..172319882-chr2:172338446..172340027,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16859394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57396064	0.88[AFR][1000 genomes]
rs57999878	0.82[AFR][1000 genomes]
rs58033547	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs58560571	0.92[AFR][1000 genomes]
rs58796565	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59745257	0.90[AFR][1000 genomes]
rs59886446	0.80[AFR][1000 genomes]
rs60100357	0.90[AFR][1000 genomes]
rs60837517	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61731491	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs62183501	0.90[AFR][1000 genomes]
rs66525413	0.81[AFR][1000 genomes]
rs73021082	0.80[AFR][1000 genomes]
rs73022904	0.90[AFR][1000 genomes]
rs73022907	0.90[AFR][1000 genomes]
rs73022921	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73022930	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73022949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7563499	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7564602	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291000-172319800	Weak transcription	Stomach Mucosa	stomach
2	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:172292600-172320400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:172293000-172318600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:172293200-172319400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:172293200-172319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:172298200-172326600	Weak transcription	Colonic Mucosa	Colon
9	chr2:172298400-172325400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:172298400-172325600	Weak transcription	Hela-S3	cervix
11	chr2:172298400-172326200	Weak transcription	NHEK	skin
12	chr2:172298400-172334400	Weak transcription	Small Intestine	intestine
13	chr2:172298400-172339400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:172298600-172341400	Weak transcription	NHLF	lung
15	chr2:172299400-172325400	Weak transcription	Gastric	stomach
16	chr2:172300600-172338600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:172304800-172325200	Weak transcription	Brain Angular Gyrus	brain
18	chr2:172304800-172325200	Weak transcription	Pancreas	Pancrea
19	chr2:172304800-172330000	Weak transcription	NH-A	brain
20	chr2:172304800-172338800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:172305000-172326400	Weak transcription	Lung	lung
22	chr2:172305800-172325200	Weak transcription	Aorta	Aorta
23	chr2:172305800-172325400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:172306000-172348000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:172306800-172325200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:172306800-172325800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:172306800-172334000	Weak transcription	Psoas Muscle	Psoas
28	chr2:172307400-172325400	Weak transcription	Thymus	Thymus
29	chr2:172307600-172325800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:172307600-172325800	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:172307800-172325000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:172307800-172341200	Weak transcription	Right Ventricle	heart
33	chr2:172308200-172325800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:172309400-172325800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:172309600-172325400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:172309600-172348400	Weak transcription	Fetal Heart	heart
37	chr2:172309800-172325200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:172309800-172325400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:172311200-172319200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:172311400-172322000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:172312000-172325400	Weak transcription	Fetal Stomach	stomach
42	chr2:172312000-172325800	Weak transcription	Fetal Brain Male	brain
43	chr2:172312400-172325400	Weak transcription	Brain Substantia Nigra	brain
44	chr2:172312600-172326800	Weak transcription	Ovary	ovary
45	chr2:172313000-172325400	Weak transcription	Fetal Brain Female	brain
46	chr2:172313000-172325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:172313200-172325600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:172313400-172339800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:172314200-172319400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:172314600-172326400	Weak transcription	Spleen	Spleen

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