Variant report

Variant	rs9839404
Chromosome Location	chr3:161015180-161015181
allele	C/T
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161006300..161011924-chr3:161012842..161019057,8	MCF-7	breast:
2	chr3:161006306..161018540-chr3:161080036..161092321,36	MCF-7	breast:
3	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
4	chr3:161004827..161016513-chr3:161081728..161095319,56	MCF-7	breast:
5	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMD3-2	chr3:161014940-161015792	NONHSAT093012

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12488318	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494261	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494844	0.87[CHB][hapmap]
rs13318781	0.94[CHB][hapmap]
rs13319969	0.84[JPT][hapmap]
rs1450519	0.83[CHB][hapmap]
rs1471440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163138	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs336544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336564	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs336565	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs336566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs336571	0.86[ASN][1000 genomes]
rs336573	0.87[ASN][1000 genomes]
rs336574	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs336576	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs336581	0.88[ASN][1000 genomes]
rs336584	0.88[ASN][1000 genomes]
rs336587	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs336588	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs336592	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs419703	0.84[ASN][1000 genomes]
rs4429651	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4487256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4490410	0.94[CHB][hapmap]
rs455739	0.86[ASN][1000 genomes]
rs458197	0.85[ASN][1000 genomes]
rs459067	0.85[ASN][1000 genomes]
rs461616	0.86[ASN][1000 genomes]
rs462081	0.86[ASN][1000 genomes]
rs57201455	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62278055	0.92[ASN][1000 genomes]
rs62279860	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62279861	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62279862	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62279892	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6795977	0.92[JPT][hapmap]
rs731363	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs73160351	0.86[ASN][1000 genomes]
rs73160362	0.93[ASN][1000 genomes]
rs73162530	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9290072	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs9290075	0.99[ASN][1000 genomes]
rs978933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9811833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825118	0.94[CHB][hapmap]
rs9827833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828231	0.88[CHB][hapmap];0.92[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9831725	0.90[ASN][1000 genomes]
rs9836094	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9857946	0.86[ASN][1000 genomes]
rs9859045	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876553	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
2	chr3:161009800-161016600	Weak transcription	Pancreas	Pancrea
3	chr3:161010400-161016600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:161015000-161016600	Weak transcription	Left Ventricle	heart
5	chr3:161015000-161017600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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