Variant report

Variant	rs10053706
Chromosome Location	chr5:80616365-80616366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10036376	0.81[CEU][hapmap]
rs10038684	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.85[CEU][hapmap]
rs1055383	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876403	0.81[CEU][hapmap]
rs17294418	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.85[CEU][hapmap]
rs2270823	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2897390	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365865	0.83[ASN][1000 genomes]
rs68077638	0.83[ASN][1000 genomes]
rs6866499	0.94[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	0.83[ASN][1000 genomes]
rs6893467	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.91[AMR][1000 genomes]
rs7448717	0.88[CEU][hapmap]
rs750728	0.85[CEU][hapmap]
rs7709071	0.83[ASN][1000 genomes]
rs7709149	0.83[ASN][1000 genomes]
rs7720009	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734902	0.83[ASN][1000 genomes]
rs9293841	0.95[CEU][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10053706	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs10053706	CTC-281B15.1	cis	Artery Aorta	GTEx
rs10053706	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs10053706	CTD-2248H3.1	cis	Thyroid	GTEx
rs10053706	CTC-281B15.1	cis	Stomach	GTEx
rs10053706	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs10053706	LOC100131067	cis	brain	BrainEAC
rs10053706	CTC-281B15.1	cis	lung	GTEx
rs10053706	CTC-281B15.1	cis	Artery Tibial	GTEx
rs10053706	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs10053706	CTD-2248H3.1	cis	lung	GTEx
rs10053706	CKMT2	cis	normal skin	skin_eQTL
rs10053706	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs10053706	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs10053706	CTC-281B15.1	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80608600-80623000	Weak transcription	Psoas Muscle	Psoas
2	chr5:80610000-80618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr5:80610600-80621800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:80611600-80623600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:80611800-80619000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:80612200-80623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:80616000-80617200	Strong transcription	Liver	Liver

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