Variant report

Variant	rs12519617
Chromosome Location	chr5:76175457-76175458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10038878	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10063816	0.81[EUR][1000 genomes]
rs10447163	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10462548	0.89[TSI][hapmap]
rs11742803	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12188004	0.95[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs12517004	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521017	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs12656576	0.84[ASN][1000 genomes]
rs13163806	0.94[EUR][1000 genomes]
rs1320306	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1320307	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1320309	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1700655	0.90[AMR][1000 genomes]
rs1700658	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1715764	0.88[AMR][1000 genomes]
rs2359426	0.90[ASN][1000 genomes]
rs2359427	0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2359428	0.86[EUR][1000 genomes]
rs2359658	0.95[CEU][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2657047	0.83[AMR][1000 genomes]
rs2681669	0.84[AMR][1000 genomes]
rs35807598	0.89[EUR][1000 genomes]
rs56975406	0.95[EUR][1000 genomes]
rs57425095	0.95[EUR][1000 genomes]
rs58093808	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60192097	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62363086	0.94[EUR][1000 genomes]
rs62363087	0.95[EUR][1000 genomes]
rs62363088	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62363089	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62363095	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6414971	0.80[CEU][hapmap]
rs6869909	0.80[TSI][hapmap]
rs6871700	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6872982	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884425	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6890905	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6896257	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7722773	0.87[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][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	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3393424	chr5:76122720-76287744	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv34133	chr5:76138696-76239330	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv524024	chr5:76166018-76187777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12519617	F2RL1	cis	multi-tissue	Pritchard
rs12519617	CRHBP	cis	uninvolved skin	skin_eQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76171000-76182400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:76171200-76175800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:76171600-76177400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:76171600-76192600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:76173400-76176000	Strong transcription	Primary hematopoietic stem cells	blood
6	chr5:76173400-76178600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:76173400-76178600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:76174600-76186400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:76174800-76175800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:76175400-76175800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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