Variant report

Variant	rs11740809
Chromosome Location	chr5:74176843-74176844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10515189	0.83[JPT][hapmap]
rs11738903	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11739301	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740706	0.86[EUR][1000 genomes]
rs11743655	0.83[JPT][hapmap]
rs11746069	0.83[JPT][hapmap]
rs11746561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs11746611	0.83[JPT][hapmap]
rs58010984	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60270014	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60430653	0.87[EUR][1000 genomes]
rs62367768	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367770	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367771	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62367773	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62367774	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62367819	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62367823	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367824	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367825	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367828	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68151843	0.86[EUR][1000 genomes]
rs7711625	0.81[EUR][1000 genomes]
rs820828	0.83[JPT][hapmap]
rs820830	0.83[JPT][hapmap]
rs820834	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518286	chr5:74169045-74243120	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv968210	chr5:74173768-74181141	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11740809	NSA2	cis	lymphoblastoid	seeQTL
rs11740809	TINP1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74172600-74179200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:74173600-74178400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:74173800-74178200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:74173800-74178200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:74173800-74178400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:74173800-74179000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:74174000-74178200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:74174000-74178400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:74174000-74181000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:74176400-74181000	Weak transcription	HepG2	liver

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