Variant report

Variant	rs249031
Chromosome Location	chr5:79766628-79766629
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	chr5:79762074..79763918-chr5:79765704..79767666,2	MCF-7	breast:
2	chr5:79765389..79768213-chr5:79774731..79777264,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10052497	0.81[EUR][1000 genomes]
rs10433	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942926	0.95[ASN][1000 genomes]
rs1097307	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097308	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1097309	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1102116	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103116	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363775	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168938	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs168939	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171595	1.00[ASN][1000 genomes]
rs171596	1.00[ASN][1000 genomes]
rs171821	0.87[EUR][1000 genomes]
rs173597	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173598	0.82[ASN][1000 genomes]
rs173599	0.95[ASN][1000 genomes]
rs174075	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1820119	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185100	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187478	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192313	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194540	0.83[ASN][1000 genomes]
rs2112152	0.86[EUR][1000 genomes]
rs2251759	0.95[ASN][1000 genomes]
rs248995	0.89[EUR][1000 genomes]
rs248999	1.00[ASN][1000 genomes]
rs249000	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249001	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249003	1.00[ASN][1000 genomes]
rs249004	1.00[ASN][1000 genomes]
rs249005	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249006	1.00[ASN][1000 genomes]
rs249015	0.92[AFR][1000 genomes]
rs249016	0.92[ASN][1000 genomes]
rs249018	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs249019	0.97[AFR][1000 genomes]
rs249020	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249021	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249023	0.95[ASN][1000 genomes]
rs249024	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249025	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249026	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249027	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249028	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249030	1.00[ASN][1000 genomes]
rs249032	1.00[ASN][1000 genomes]
rs249033	0.89[AFR][1000 genomes]
rs249037	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249038	0.95[ASN][1000 genomes]
rs249039	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249040	0.93[AFR][1000 genomes]
rs2544592	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544593	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544598	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544599	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544600	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544603	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544604	0.95[ASN][1000 genomes]
rs2547487	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2547497	0.83[EUR][1000 genomes]
rs259023	0.85[ASN][1000 genomes]
rs259024	0.85[ASN][1000 genomes]
rs259025	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259026	0.85[ASN][1000 genomes]
rs259027	0.85[ASN][1000 genomes]
rs259028	0.95[ASN][1000 genomes]
rs259029	0.95[ASN][1000 genomes]
rs259030	0.95[ASN][1000 genomes]
rs259031	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259032	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs259033	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259034	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259035	0.83[EUR][1000 genomes]
rs259041	0.88[EUR][1000 genomes]
rs259043	0.89[EUR][1000 genomes]
rs259052	0.82[ASN][1000 genomes]
rs259055	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2599508	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095850	0.89[AFR][1000 genomes]
rs3095851	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096111	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs394076	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394170	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399261	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs408899	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704674	0.95[ASN][1000 genomes]
rs557346	1.00[ASN][1000 genomes]
rs701380	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835726	0.82[ASN][1000 genomes]
rs835729	0.87[ASN][1000 genomes]
rs835731	0.82[EUR][1000 genomes]
rs856765	0.95[ASN][1000 genomes]
rs856772	1.00[ASN][1000 genomes]
rs863163	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969567	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79731400-79768000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:79733400-79782600	Weak transcription	NHLF	lung
3	chr5:79744800-79783200	Weak transcription	Colonic Mucosa	Colon
4	chr5:79753400-79769600	Weak transcription	HUVEC	blood vessel
5	chr5:79754600-79769600	Weak transcription	Osteobl	bone
6	chr5:79755600-79768000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:79757000-79770000	Weak transcription	NHDF-Ad	bronchial
8	chr5:79757400-79769400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:79759400-79767800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:79759400-79768800	Weak transcription	NH-A	brain
11	chr5:79759400-79775000	Weak transcription	Hela-S3	cervix
12	chr5:79759400-79778800	Weak transcription	Small Intestine	intestine
13	chr5:79759400-79779200	Weak transcription	Lung	lung
14	chr5:79759400-79782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:79760200-79766800	Strong transcription	Liver	Liver
16	chr5:79762600-79769200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:79763000-79769800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:79763200-79767400	Weak transcription	Aorta	Aorta
19	chr5:79763200-79772400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:79763200-79779600	Weak transcription	Gastric	stomach
21	chr5:79763400-79775200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:79763600-79767400	Weak transcription	HSMMtube	muscle
23	chr5:79764000-79767800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:79764000-79768200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:79764000-79771400	Strong transcription	Brain Angular Gyrus	brain
26	chr5:79764200-79768000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:79764200-79775200	Weak transcription	HMEC	breast
28	chr5:79764400-79770200	Weak transcription	HepG2	liver
29	chr5:79764800-79768200	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr5:79764800-79771800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:79764800-79772000	Strong transcription	Left Ventricle	heart
32	chr5:79765000-79766800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr5:79765000-79766800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:79765000-79766800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr5:79765000-79766800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:79765000-79766800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:79765000-79766800	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr5:79765000-79767000	ZNF genes & repeats	Adipose Nuclei	Adipose
39	chr5:79765000-79768000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr5:79765000-79768200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
41	chr5:79765000-79768200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:79765000-79768200	Strong transcription	Ovary	ovary
43	chr5:79765000-79768400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr5:79765000-79768400	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr5:79765000-79768400	ZNF genes & repeats	Dnd41	blood
46	chr5:79765000-79769000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:79765000-79776000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:79765200-79766800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:79765200-79768200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:79765400-79767800	Weak transcription	Brain Inferior Temporal Lobe	brain

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