Variant report

Variant	rs11708154
Chromosome Location	chr3:179635808-179635809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11709733	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11718907	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1404271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1599791	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16830940	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17691911	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17748709	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17748864	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2302741	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302742	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28619517	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41265425	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4146789	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56263652	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56395499	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56677569	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56836862	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57376419	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57823511	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59018122	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59453720	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73058681	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73060731	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73060760	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73060761	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630877	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7637613	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7646149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290685	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs940523	1.00[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9682757	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9831383	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9836757	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11708154	KCNMB2	cis	parietal	SCAN
rs11708154	PSMD2	cis	cerebellum	SCAN
rs11708154	PTRH2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179624800-179639000	Weak transcription	Brain Substantia Nigra	brain
2	chr3:179630000-179638800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:179633000-179638800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:179633400-179636800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:179634200-179636600	Weak transcription	Dnd41	blood

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