Variant report

Variant	rs3740279
Chromosome Location	chr10:90122512-90122513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10736351	1.00[YRI][hapmap]
rs10887807	0.92[ASN][1000 genomes]
rs11202703	0.84[ASN][1000 genomes]
rs11202705	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11202706	0.86[ASN][1000 genomes]
rs11202722	0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs11202726	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11202731	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11202734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11528433	0.86[ASN][1000 genomes]
rs11598623	0.90[ASN][1000 genomes]
rs12217988	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12219831	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12220632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12221213	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs12569922	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12572813	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs1426617	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs1582223	0.89[ASN][1000 genomes]
rs1582224	0.82[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1613409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1648512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648523	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs17111200	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs1774970	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1774971	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2195013	0.84[ASN][1000 genomes]
rs2209553	1.00[YRI][hapmap]
rs2241515	0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2576159	1.00[YRI][hapmap]
rs2765456	1.00[YRI][hapmap]
rs3781201	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs55749454	0.89[ASN][1000 genomes]
rs57949777	0.82[ASN][1000 genomes]
rs59184458	0.82[ASN][1000 genomes]
rs59482232	0.82[ASN][1000 genomes]
rs61260851	0.82[ASN][1000 genomes]
rs7073755	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7075138	0.90[ASN][1000 genomes]
rs7097606	0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs74149704	0.91[ASN][1000 genomes]
rs74149712	0.82[ASN][1000 genomes]
rs74149714	0.91[ASN][1000 genomes]
rs74149715	0.91[ASN][1000 genomes]
rs752709	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7919335	0.84[ASN][1000 genomes]
rs792224	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs792225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs792227	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs792228	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792229	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs792232	0.82[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs880793	0.89[ASN][1000 genomes]
rs880794	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv551838	chr10:90058637-90137045	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3740279	LIPF	cis	cerebellum	SCAN
rs3740279	ATAD1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90117400-90129200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr10:90120000-90123400	Weak transcription	Aorta	Aorta
3	chr10:90120800-90122600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:90122000-90126200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr10:90122400-90122600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:90122400-90122800	Enhancers	Liver	Liver

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