Variant report

Variant	rs4491016
Chromosome Location	chr1:47394096-47394097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11211366	0.88[CHD][hapmap]
rs11211402	0.93[EUR][1000 genomes]
rs11211408	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11576162	0.92[CEU][hapmap];0.88[CHD][hapmap]
rs11576656	0.85[ASN][1000 genomes]
rs12408938	0.85[JPT][hapmap]
rs1847229	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1890251	0.83[CHD][hapmap]
rs2065996	0.85[CHD][hapmap]
rs2185032	0.84[CEU][hapmap]
rs2405335	0.89[CHD][hapmap]
rs3766196	0.92[CEU][hapmap];0.91[CHD][hapmap]
rs3766197	1.00[CEU][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap]
rs3820080	1.00[CEU][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap]
rs3890010	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4646486	0.84[CEU][hapmap];0.86[CHD][hapmap]
rs4646487	0.92[CEU][hapmap];0.86[CHD][hapmap]
rs4646492	0.92[CEU][hapmap];0.89[CHD][hapmap]
rs4646493	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[TSI][hapmap]
rs4646495	0.92[CEU][hapmap];0.91[CHD][hapmap];0.84[TSI][hapmap]
rs4660979	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660980	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4660983	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57025390	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57791728	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6672252	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6687264	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67392104	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs837395	0.86[CHD][hapmap]
rs9332998	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9333027	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9333029	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv945928	chr1:47392738-47414613	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4491016	PTPRF	cis	cerebellum	SCAN
rs4491016	HECTD3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47393200-47400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47393800-47394400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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