Variant report

Variant	rs9878564
Chromosome Location	chr3:51845226-51845227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs13321674	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs13325153	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs13325762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13327225	1.00[MEX][hapmap]
rs17051832	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs17081501	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1857801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28776255	0.92[AFR][1000 genomes]
rs61011489	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61048512	0.92[AFR][1000 genomes]
rs61299098	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6781310	0.86[AFR][1000 genomes]
rs6789601	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6792143	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6803994	0.84[AFR][1000 genomes]
rs6806124	1.00[MEX][hapmap]
rs6806593	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6806812	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7623760	0.95[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7632944	0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs975258	0.90[YRI][hapmap]
rs9809757	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9815475	0.87[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap]
rs9820804	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822619	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822994	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823975	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9831594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839703	0.91[AFR][1000 genomes]
rs9840747	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9842066	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9846102	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9856180	0.95[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs9858279	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9859656	0.85[YRI][hapmap]
rs9859820	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9863019	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877178	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9880050	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9880623	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9880631	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv3416846	chr3:51781117-51888179	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51836800-51847600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:51842400-51845800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:51845200-51845400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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