Variant report

Variant	rs398274
Chromosome Location	chr5:16586481-16586482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16577162..16580474-chr5:16583638..16586521,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs173963	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173972	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650584	0.97[ASN][1000 genomes]
rs17650599	0.97[ASN][1000 genomes]
rs17650706	0.94[ASN][1000 genomes]
rs17707133	1.00[ASN][1000 genomes]
rs2447809	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2447810	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2447811	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2447812	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447813	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447815	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447816	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447817	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447818	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451848	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451849	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451850	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451852	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451853	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451854	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451855	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451856	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560825	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256878	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617419	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431154	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448021	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604535	1.00[ASN][1000 genomes]
rs62369751	0.97[ASN][1000 genomes]
rs62371269	1.00[ASN][1000 genomes]
rs62371271	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:16571400-16587200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr5:16571400-16588200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:16574800-16589800	Weak transcription	Thymus	Thymus
6	chr5:16575000-16588000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:16575600-16591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:16575800-16587600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:16576000-16587200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:16578400-16606800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:16579200-16586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:16579400-16593200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:16581000-16598400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:16581200-16588600	Weak transcription	Fetal Heart	heart
15	chr5:16581400-16587000	Weak transcription	Primary T cells from cord blood	blood
16	chr5:16581400-16593200	Weak transcription	Right Ventricle	heart
17	chr5:16581400-16596000	Weak transcription	Fetal Brain Female	brain
18	chr5:16583400-16591400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:16583400-16599600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:16584400-16591200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:16584400-16592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:16585200-16586800	Enhancers	Brain Hippocampus Middle	brain
23	chr5:16585400-16586800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr5:16585400-16615600	Weak transcription	Primary B cells from cord blood	blood
25	chr5:16585600-16586600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:16585600-16588000	Weak transcription	Liver	Liver
27	chr5:16585600-16588000	Weak transcription	Psoas Muscle	Psoas
28	chr5:16585600-16588400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:16585600-16588400	Weak transcription	Pancreas	Pancrea
30	chr5:16585600-16588400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:16585600-16588400	Weak transcription	HepG2	liver
32	chr5:16585600-16600000	Weak transcription	Gastric	stomach
33	chr5:16585800-16586800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:16585800-16587800	Weak transcription	Lung	lung
35	chr5:16585800-16588400	Weak transcription	Brain Angular Gyrus	brain
36	chr5:16585800-16588400	Weak transcription	Stomach Mucosa	stomach
37	chr5:16585800-16605000	Weak transcription	Fetal Intestine Large	intestine
38	chr5:16586000-16586600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:16586000-16586600	Enhancers	Brain Cingulate Gyrus	brain
40	chr5:16586000-16588000	Weak transcription	Left Ventricle	heart
41	chr5:16586000-16594800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:16586200-16586600	Enhancers	Brain Germinal Matrix	brain
43	chr5:16586200-16586800	Enhancers	Brain Anterior Caudate	brain
44	chr5:16586200-16587000	Enhancers	Primary B cells from peripheral blood	blood
45	chr5:16586400-16586600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr5:16586400-16587800	Weak transcription	Brain Substantia Nigra	brain

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