Variant report

Variant	rs7874762
Chromosome Location	chr9:17689047-17689048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1000770	0.95[CHB][hapmap];0.84[AMR][1000 genomes]
rs10118522	0.95[CHB][hapmap]
rs10738482	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10738485	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs10756895	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756896	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756910	0.87[CHB][hapmap]
rs10810817	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10810818	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810821	0.95[CHB][hapmap]
rs10810822	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap]
rs10810828	0.95[CHB][hapmap]
rs10963190	0.91[CHB][hapmap]
rs10963191	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10963196	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10963210	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536064	0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs1536065	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1536066	0.95[CHB][hapmap]
rs1536069	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2025557	0.82[MEX][hapmap]
rs2025559	0.81[EUR][1000 genomes]
rs2147729	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2147735	0.91[CHB][hapmap]
rs2147736	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2182083	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2182084	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs2182085	0.86[CHB][hapmap]
rs2182086	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs2182087	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2182090	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2209433	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2209434	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2209435	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2209437	0.85[TSI][hapmap]
rs2383044	0.87[CHB][hapmap]
rs3780232	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs3780234	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs3780235	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780236	0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3808700	0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3808704	0.95[CHB][hapmap]
rs3808707	0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808708	0.95[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808709	0.95[CHB][hapmap]
rs3808711	0.82[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs3808712	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs3808713	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs3808714	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3808716	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3808717	0.95[CHB][hapmap]
rs3808718	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap]
rs3808719	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3808720	0.81[CEU][hapmap];0.91[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3808721	0.85[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3808723	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808726	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs3824383	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs4418424	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs4578059	0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4601434	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs67384654	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7020158	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7021836	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7031459	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7036904	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs717373	0.87[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7350202	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7847174	0.81[EUR][1000 genomes]
rs7847297	0.87[EUR][1000 genomes]
rs7856894	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7858624	0.94[CHB][hapmap]
rs7862689	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866654	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7866898	0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7870919	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs7875763	0.92[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs961372	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs998599	0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7874762	IFNA2	cis	parietal	SCAN
rs7874762	IFNA8	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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