Variant report

Variant	rs62279120
Chromosome Location	chr3:19927880-19927881
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	chr3:19926188..19928582-chr3:19987242..19988957,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10155054	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927871	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180771	0.91[ASN][1000 genomes]
rs17574049	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872737	1.00[ASN][1000 genomes]
rs2101390	1.00[ASN][1000 genomes]
rs3849533	0.91[ASN][1000 genomes]
rs3916092	1.00[ASN][1000 genomes]
rs4858712	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858713	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858714	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55669125	0.91[ASN][1000 genomes]
rs55829813	1.00[ASN][1000 genomes]
rs56004950	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572420	0.91[ASN][1000 genomes]
rs62279119	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279122	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279123	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279125	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279132	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279134	1.00[ASN][1000 genomes]
rs62279135	1.00[ASN][1000 genomes]
rs62279136	1.00[ASN][1000 genomes]
rs62279138	1.00[ASN][1000 genomes]
rs6550213	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66526230	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046020	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809548	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810613	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription 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 target site	17 gene(s)	inside rSNPs	diseases
6	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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 target site	17 gene(s)	inside rSNPs	diseases
10	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv1003183	chr3:19671647-19948351	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62279120	EFHB	cis	lung	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19923400-19930000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:19924200-19930200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:19926800-19928400	Enhancers	HepG2	liver
4	chr3:19926800-19928800	Enhancers	A549	lung
5	chr3:19927000-19930400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:19927000-19930600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:19927400-19930000	Weak transcription	K562	blood
8	chr3:19927400-19930400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:19927400-19941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:19927600-19928200	Enhancers	Ovary	ovary
11	chr3:19927600-19928400	Enhancers	Liver	Liver
12	chr3:19927600-19930600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:19927800-19928200	Weak transcription	Muscle Satellite Cultured Cells	--

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