Variant report

Variant	rs940522
Chromosome Location	chr3:179712132-179712133
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11713683	0.99[ASN][1000 genomes]
rs13324196	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13325206	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1522115	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1851351	0.86[ASN][1000 genomes]
rs2056598	0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2204095	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs2339932	0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs56397887	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57729381	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59205301	0.83[AMR][1000 genomes]
rs61623675	0.80[ASN][1000 genomes]
rs6443685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443687	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6443688	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6764772	0.88[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs6787707	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6797922	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs6800148	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883444	0.83[EUR][1000 genomes]
rs73883446	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73883462	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73883468	0.99[ASN][1000 genomes]
rs73883469	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73883479	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7614706	0.86[ASN][1000 genomes]
rs7615924	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630527	0.99[ASN][1000 genomes]
rs939824	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs939825	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9809603	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816641	0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9823631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826864	0.93[JPT][hapmap]
rs9828621	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9833738	0.80[ASN][1000 genomes]
rs9856007	0.88[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs9858631	0.86[ASN][1000 genomes]
rs9866193	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs9870941	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881655	0.99[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	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
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs940522	CHRD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179700800-179721000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:179703800-179725200	Weak transcription	Dnd41	blood
3	chr3:179710400-179725600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:179710600-179721000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:179710800-179720400	Weak transcription	Brain Hippocampus Middle	brain

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