Variant report

Variant	rs62404977
Chromosome Location	chr5:179428887-179428888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179423298..179424823-chr5:179427482..179429266,2	MCF-7	breast:
2	chr5:179426841..179429316-chr5:179431530..179434128,2	MCF-7	breast:
3	chr5:179427967..179430007-chr5:179432623..179435303,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10051694	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10056991	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10059400	0.87[EUR][1000 genomes]
rs10066845	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10071652	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10079029	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10464058	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11249663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249664	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249665	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748441	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11750102	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13435998	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17681274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776946	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776948	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4235505	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4264913	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700852	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700854	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57008562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57117216	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61356660	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62404970	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62404974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62404976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404979	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405015	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601077	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601078	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6862105	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6869349	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873317	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873639	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884565	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7729516	0.87[EUR][1000 genomes]
rs7734329	0.81[EUR][1000 genomes]
rs9329095	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:179405200-179429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:179422400-179429600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:179425000-179439400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:179426200-179440000	Weak transcription	Primary T cells from cord blood	blood
9	chr5:179426400-179433400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:179426400-179438400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:179426400-179447200	Weak transcription	A549	lung
12	chr5:179426600-179433800	Weak transcription	Fetal Heart	heart
13	chr5:179426800-179429000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:179426800-179429800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:179427000-179429000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
16	chr5:179427000-179433600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:179427000-179439600	Weak transcription	NHEK	skin
18	chr5:179427000-179447400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:179427200-179429000	Strong transcription	Fetal Brain Female	brain
20	chr5:179427200-179430400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:179427200-179430400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:179427400-179430200	Strong transcription	Primary hematopoietic stem cells	blood
23	chr5:179427400-179447200	Weak transcription	Hela-S3	cervix
24	chr5:179427600-179435200	Weak transcription	Small Intestine	intestine
25	chr5:179427800-179429000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:179427800-179429800	Strong transcription	Liver	Liver
27	chr5:179427800-179429800	Strong transcription	Placenta	Placenta
28	chr5:179427800-179430400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:179427800-179430400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:179427800-179433200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:179428000-179429000	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:179428000-179429800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:179428000-179429800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:179428000-179429800	ZNF genes & repeats	Aorta	Aorta
35	chr5:179428000-179429800	Genic enhancers	Brain Substantia Nigra	brain
36	chr5:179428000-179429800	Genic enhancers	Right Ventricle	heart
37	chr5:179428000-179430400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:179428000-179430400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:179428000-179430400	Strong transcription	Fetal Stomach	stomach
40	chr5:179428000-179430600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:179428000-179431600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr5:179428200-179429000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr5:179428200-179429000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr5:179428200-179429000	Strong transcription	HepG2	liver
45	chr5:179428200-179429200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:179428200-179429200	ZNF genes & repeats	Lung	lung
47	chr5:179428200-179429600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:179428200-179429600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:179428200-179429600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:179428200-179429800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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