Variant report

Variant	rs17458061
Chromosome Location	chr11:57786071-57786072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1031232	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap]
rs11822108	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs11824895	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12417338	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418614	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419427	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12419849	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap]
rs12420385	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12421556	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1349483	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1447167	0.81[MEX][hapmap]
rs1447182	0.95[CEU][hapmap]
rs17538527	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap]
rs2175276	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2441964	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap]
rs2866831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41325844	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs55665208	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023680	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56245847	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61903961	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61903969	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904010	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61904013	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61904025	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs61904041	0.84[AFR][1000 genomes]
rs61905316	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61905341	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905342	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905343	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905344	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905345	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107162	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap]
rs7108167	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7112942	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7128781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72915744	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72917859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72919837	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7925491	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942438	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7944888	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945120	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921443	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv328	chr11:57744748-57789940	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv975361	chr11:57761225-57786621	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2761678	chr11:57768288-57810886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17458061	OR8K1	cis	parietal	SCAN
rs17458061	OR5AS1	cis	parietal	SCAN
rs17458061	MS4A7	cis	cerebellum	SCAN
rs17458061	YPEL4	cis	multi-tissue	Pritchard
rs17458061	MS4A6A	cis	cerebellum	SCAN
rs17458061	CCDC86	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57785800-57791400	Weak transcription	Pancreas	Pancrea
2	chr11:57786000-57787200	Weak transcription	Left Ventricle	heart

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