Variant report

Variant	rs1449336
Chromosome Location	chr3:54203510-54203511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11712475	1.00[ASN][1000 genomes]
rs11716284	1.00[JPT][hapmap]
rs11716674	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11718407	0.90[ASN][1000 genomes]
rs12489940	1.00[ASN][1000 genomes]
rs12493260	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12493623	0.95[ASN][1000 genomes]
rs12630117	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4076707	0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4076709	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4373100	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4408898	0.95[ASN][1000 genomes]
rs4428220	0.95[ASN][1000 genomes]
rs4428221	0.95[ASN][1000 genomes]
rs4927998	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928004	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4928006	0.81[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes]
rs6445630	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765381	0.95[CEU][hapmap]
rs6809942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73085903	1.00[ASN][1000 genomes]
rs73085927	0.90[ASN][1000 genomes]
rs7639142	0.95[ASN][1000 genomes]
rs9880023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1449336	TMEM110	cis	cerebellum	SCAN
rs1449336	SPATA12	cis	cerebellum	SCAN
rs1449336	C3orf51	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54200400-54205400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:54200400-54214800	Weak transcription	Psoas Muscle	Psoas
3	chr3:54202800-54205200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:54203000-54203600	Weak transcription	Lung	lung

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