Variant report

Variant	rs17111200
Chromosome Location	chr10:90101828-90101829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10887807	0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11202703	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11202705	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11202706	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11202722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11202726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11202731	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11202734	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11528433	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11598623	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12217988	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs12219687	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12219831	0.81[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs12220632	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs12221213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12572813	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1426617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1582223	0.85[ASN][1000 genomes]
rs1582224	0.90[CHD][hapmap];0.88[JPT][hapmap]
rs1613409	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1648512	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs1648523	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1774970	0.81[JPT][hapmap]
rs1774971	0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2195013	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740279	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs3781201	0.85[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs55749454	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59513062	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7075138	0.87[ASN][1000 genomes]
rs7086211	0.84[EUR][1000 genomes]
rs7097606	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs74149704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74149714	0.83[ASN][1000 genomes]
rs74149715	0.83[ASN][1000 genomes]
rs752709	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7919335	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs792224	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs792225	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs792227	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs792228	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs792229	0.86[ASN][1000 genomes]
rs792232	0.90[CHD][hapmap];0.88[JPT][hapmap]
rs880793	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs880794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17111200	ATAD1	cis	parietal	SCAN
rs17111200	TBC1D22A	cis	Cerebellum	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90084600-90103600	Weak transcription	Ovary	ovary
2	chr10:90099800-90103600	Weak transcription	Aorta	Aorta
3	chr10:90100000-90103600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:90101800-90102000	Enhancers	Right Atrium	heart
5	chr10:90101800-90104000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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