Variant report

Variant	rs3808700
Chromosome Location	chr9:17697976-17697977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1000770	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10118522	0.86[CHB][hapmap]
rs10738482	0.91[CHB][hapmap];0.91[MEX][hapmap]
rs10738485	0.86[CHB][hapmap];0.91[MEX][hapmap]
rs10756895	0.87[EUR][1000 genomes]
rs10756896	0.90[CHB][hapmap]
rs10756910	0.86[CHB][hapmap]
rs10810817	0.82[MEX][hapmap]
rs10810821	0.86[CHB][hapmap]
rs10810822	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs10810828	0.86[CHB][hapmap]
rs10963190	0.82[CHB][hapmap]
rs10963210	0.91[CHB][hapmap]
rs12341417	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1536066	0.95[CHB][hapmap]
rs1536073	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs2025557	0.95[MEX][hapmap];0.84[TSI][hapmap]
rs2147735	0.91[CHB][hapmap]
rs2147736	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs2182084	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs2182086	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs2182087	0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs2182090	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2209433	0.86[CHB][hapmap];0.82[MEX][hapmap]
rs2209434	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2209435	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs2209437	0.91[MEX][hapmap]
rs2383044	0.86[CHB][hapmap]
rs3780232	0.86[CHB][hapmap];0.91[MEX][hapmap]
rs3780234	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs3780235	0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780236	0.82[CHB][hapmap]
rs3808690	0.82[MEX][hapmap]
rs3808704	0.86[CHB][hapmap]
rs3808707	0.86[CHB][hapmap]
rs3808708	0.86[CHB][hapmap];0.91[MEX][hapmap]
rs3808709	0.86[CHB][hapmap]
rs3808711	0.86[CHB][hapmap];0.86[MEX][hapmap]
rs3808712	0.86[CHB][hapmap];0.91[MEX][hapmap]
rs3808713	0.86[CHB][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs3808714	0.91[CHB][hapmap]
rs3808716	0.86[CHB][hapmap]
rs3808717	0.86[CHB][hapmap]
rs3808718	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs3808719	0.86[CHB][hapmap]
rs3808720	0.82[CHB][hapmap];0.87[MEX][hapmap]
rs3808721	0.82[CHB][hapmap]
rs3808723	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs3824383	0.81[CHB][hapmap]
rs4418424	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4578059	0.82[CHB][hapmap]
rs4601434	0.86[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7020158	0.90[CHB][hapmap];0.86[EUR][1000 genomes]
rs7021836	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7031459	0.81[EUR][1000 genomes]
rs7036904	0.80[JPT][hapmap]
rs717373	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7856894	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7858624	0.87[CHB][hapmap]
rs7862689	0.86[EUR][1000 genomes]
rs7866654	0.83[EUR][1000 genomes]
rs7866898	0.83[EUR][1000 genomes]
rs7870919	0.81[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs7874762	0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap]
rs7875763	0.81[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs961372	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs998599	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892674	chr9:17631186-17699981	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv1016971	chr9:17648242-17720176	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv1021022	chr9:17649360-17723730	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv892675	chr9:17694823-17790526	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3808700	IFNA2	cis	parietal	SCAN
rs3808700	IFNA8	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17695800-17699800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:17696200-17699400	Weak transcription	Fetal Brain Male	brain

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