Variant report

Variant	rs9309819
Chromosome Location	chr3:78848032-78848033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11127634	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495127	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13087237	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1480687	0.84[CEU][hapmap]
rs1480688	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1487139	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1623449	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs162870	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1840969	0.82[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1843786	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs28629289	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs333481	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs333491	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs333495	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs365165	0.81[ASN][1000 genomes]
rs416551	0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs439325	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs444598	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs510006	0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs6762005	0.84[JPT][hapmap]
rs9309818	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9309820	0.84[CEU][hapmap]
rs9631512	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9835958	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9837982	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861264	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9873248	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877603	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9881587	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv432459	chr3:78819310-78874310	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78841200-78850600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:78841400-78851600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:78841600-78850800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:78843800-78850800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:78844200-78852800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:78844200-78853600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:78844400-78854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:78846600-78850800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:78846600-78850800	Weak transcription	Fetal Lung	lung
10	chr3:78846600-78851000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:78846800-78850200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:78846800-78851200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:78846800-78851200	Weak transcription	Primary T cells from cord blood	blood
14	chr3:78847400-78848200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:78847400-78848400	Enhancers	HepG2	liver

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