Variant report

Variant	rs62279892
Chromosome Location	chr3:161028330-161028331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161025819..161030681-chr3:161030815..161036788,8	MCF-7	breast:
2	chr3:161026332..161029255-chr3:161034425..161036502,2	MCF-7	breast:
3	chr3:161023364..161025630-chr3:161026423..161028838,2	MCF-7	breast:
4	chr3:161027478..161029275-chr3:161031278..161032778,2	MCF-7	breast:
5	chr3:160995856..160997723-chr3:161026666..161029126,2	MCF-7	breast:
6	chr3:161025355..161028351-chr3:161131512..161133073,2	MCF-7	breast:
7	chr3:161025866..161029285-chr3:161088973..161091892,6	MCF-7	breast:
8	chr3:160472534..160474749-chr3:161027522..161029214,2	MCF-7	breast:
9	chr3:161026928..161036306-chr3:161081784..161094254,31	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12488318	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12494261	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471440	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1478567	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs163138	0.81[ASN][1000 genomes]
rs336544	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs336545	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs336546	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs336564	0.81[ASN][1000 genomes]
rs336565	0.81[ASN][1000 genomes]
rs336566	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336581	0.81[ASN][1000 genomes]
rs336584	0.81[ASN][1000 genomes]
rs336587	0.81[ASN][1000 genomes]
rs336588	0.81[ASN][1000 genomes]
rs336592	0.81[ASN][1000 genomes]
rs4429651	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4487256	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs462081	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57201455	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62279860	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62279861	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62279862	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73162530	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9290075	0.82[ASN][1000 genomes]
rs978933	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9811833	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9812083	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9827833	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9828189	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9828231	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9836094	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9839404	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9859045	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9876553	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161017000-161033000	Weak transcription	Left Ventricle	heart
2	chr3:161017600-161032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:161025400-161031800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:161026400-161031600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:161026600-161032400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:161027000-161029200	Enhancers	Primary T cells from cord blood	blood
7	chr3:161027000-161032000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:161027000-161032600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:161027000-161032800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:161027200-161029000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:161027200-161031200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:161027200-161032600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:161027800-161029800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:161027800-161031800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:161028000-161029200	Enhancers	GM12878-XiMat	blood
16	chr3:161028000-161030800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:161028000-161031200	Enhancers	Dnd41	blood
18	chr3:161028200-161028600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:161028200-161028600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr3:161028200-161031400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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