Variant report

Variant	rs62404970
Chromosome Location	chr5:179404114-179404115
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	chr5:179402276..179404351-chr5:179406069..179408902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10051694	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10056991	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10059400	0.86[EUR][1000 genomes]
rs10066845	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10071652	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10079029	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10464058	0.90[EUR][1000 genomes]
rs11249663	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249664	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11249665	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11739706	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11739898	0.86[AFR][1000 genomes]
rs11748441	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11750102	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435998	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17681274	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776946	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776948	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235505	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4264913	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4700852	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4700854	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57008562	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57117216	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61356660	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62404974	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62404976	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62404977	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62404979	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62405015	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601077	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601078	0.95[EUR][1000 genomes]
rs6862105	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6869349	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873317	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873639	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6884565	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7729516	0.86[EUR][1000 genomes]
rs7734329	0.81[EUR][1000 genomes]
rs9329095	0.83[AMR][1000 genomes];0.95[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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
2	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
3	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:179381200-179405600	Weak transcription	NHLF	lung
5	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:179383200-179408600	Weak transcription	A549	lung
7	chr5:179388800-179405000	Weak transcription	HUVEC	blood vessel
8	chr5:179388800-179405800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:179389000-179405800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:179389400-179411400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179391800-179406200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:179392600-179414800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:179394400-179405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:179395000-179405600	Weak transcription	Stomach Mucosa	stomach
15	chr5:179396600-179404200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:179396600-179461800	Weak transcription	HSMM	muscle
17	chr5:179399000-179406800	Strong transcription	Fetal Muscle Leg	muscle
18	chr5:179399000-179408000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:179399000-179408400	Strong transcription	Brain Germinal Matrix	brain
20	chr5:179399200-179405200	Strong transcription	Pancreas	Pancrea
21	chr5:179399200-179405800	Strong transcription	Adipose Nuclei	Adipose
22	chr5:179399200-179406800	Strong transcription	Fetal Stomach	stomach
23	chr5:179399400-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:179399400-179408000	Strong transcription	Left Ventricle	heart
25	chr5:179399400-179408200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:179399800-179408400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:179400000-179405000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:179400000-179405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:179400000-179408400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:179400000-179411400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:179400200-179406000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:179400200-179407000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:179400200-179408200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:179400200-179408400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:179400400-179405200	Strong transcription	Fetal Intestine Small	intestine
36	chr5:179400400-179405800	Strong transcription	Right Ventricle	heart
37	chr5:179400400-179406600	Weak transcription	Dnd41	blood
38	chr5:179400400-179406800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr5:179400400-179407400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:179400400-179408000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr5:179400400-179408400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:179400400-179412200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:179400600-179405200	Strong transcription	Placenta	Placenta
44	chr5:179400600-179405800	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr5:179400600-179408200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:179400600-179408200	Strong transcription	Lung	lung
47	chr5:179400600-179408400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:179400800-179405200	Strong transcription	Colon Smooth Muscle	Colon
49	chr5:179400800-179405800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:179400800-179405800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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