Variant report

Variant	rs684117
Chromosome Location	chr1:75711719-75711720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493561	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493570	1.00[CHB][hapmap]
rs12117429	1.00[ASN][1000 genomes]
rs12132601	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133614	1.00[CHB][hapmap]
rs12138223	1.00[CHB][hapmap]
rs12142460	1.00[CHB][hapmap]
rs12732329	1.00[CHB][hapmap]
rs12751207	1.00[CHB][hapmap]
rs1319656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405312	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526511	1.00[CHB][hapmap]
rs1526516	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565565	1.00[ASN][1000 genomes]
rs17640591	1.00[ASN][1000 genomes]
rs1852348	1.00[CHB][hapmap]
rs1852349	1.00[CHB][hapmap]
rs4949821	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949838	0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs595009	0.86[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607167	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610159	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659170	0.86[EUR][1000 genomes]
rs6695423	1.00[CHB][hapmap]
rs677470	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679258	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74094382	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524020	1.00[CHB][hapmap]

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	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997508	chr1:75709664-75748920	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs684117	PTGFR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75701200-75715800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:75710600-75714600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:75710800-75711800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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