Variant report

Variant	rs1426618
Chromosome Location	chr10:90076715-90076716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89621287..89622791-chr10:90075182..90076872,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10887800	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887801	0.83[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs10887802	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10887803	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887804	0.88[ASN][1000 genomes]
rs10887805	0.89[ASN][1000 genomes]
rs10887806	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11202702	0.86[CHB][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs11202712	0.94[ASN][1000 genomes]
rs11202713	0.94[ASN][1000 genomes]
rs11202715	0.90[ASN][1000 genomes]
rs11202716	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11202723	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1346226	0.83[CHB][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1426619	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs1582784	0.86[ASN][1000 genomes]
rs4933476	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61853517	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6586125	0.93[ASN][1000 genomes]
rs7069120	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7089911	0.83[CHB][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs7091137	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7096330	0.86[ASN][1000 genomes]
rs7895582	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7895674	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7899861	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7905573	0.83[ASN][1000 genomes]
rs7905600	0.90[ASN][1000 genomes]
rs7917640	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs796945	0.84[CHD][hapmap]
rs919115	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1426618	IFIT2	cis	parietal	SCAN
rs1426618	PAPSS2	cis	parietal	SCAN
rs1426618	SNCG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90076200-90078200	Weak transcription	Thymus	Thymus
2	chr10:90076200-90078600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr10:90076400-90078000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr10:90076400-90078000	Weak transcription	Dnd41	blood
5	chr10:90076600-90077600	Weak transcription	Fetal Thymus	thymus

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