Variant report

Variant	rs62308027
Chromosome Location	chr4:79098779-79098780
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	chr4:79097455..79099663-chr4:79105000..79107358,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11098084	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098085	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12645741	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12649696	0.81[AMR][1000 genomes]
rs13133150	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17003021	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003028	0.84[EUR][1000 genomes]
rs17003043	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17420789	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4558894	0.92[ASN][1000 genomes]
rs58427733	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58661619	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60419354	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62308039	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv879502	chr4:79052851-79144309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv829977	chr4:79082318-79110300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv999844	chr4:79092549-79165869	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79090200-79104200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:79095200-79099000	Enhancers	Fetal Intestine Large	intestine
3	chr4:79095400-79099200	Enhancers	HepG2	liver
4	chr4:79096200-79099000	Enhancers	Fetal Intestine Small	intestine
5	chr4:79096200-79106200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:79096400-79098800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:79096600-79100000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:79096600-79100200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:79096800-79099200	Enhancers	Placenta	Placenta
10	chr4:79097000-79099400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:79097000-79104400	Weak transcription	Psoas Muscle	Psoas
12	chr4:79097200-79098800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:79097200-79100000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:79097200-79100000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:79097200-79100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:79097200-79100000	Weak transcription	Lung	lung
17	chr4:79097200-79102000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:79097200-79108400	Weak transcription	Pancreas	Pancrea
19	chr4:79097400-79098800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr4:79097400-79099200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:79097600-79099000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:79097600-79099200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:79097800-79106000	Weak transcription	Fetal Kidney	kidney
24	chr4:79097800-79106200	Weak transcription	Fetal Lung	lung
25	chr4:79098200-79099000	Enhancers	A549	lung
26	chr4:79098200-79099800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:79098200-79099800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:79098200-79100000	Weak transcription	NHEK	skin
29	chr4:79098200-79100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:79098200-79100200	Weak transcription	HMEC	breast
31	chr4:79098600-79099200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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