Variant report

Variant	rs1423785
Chromosome Location	chr16:65219154-65219155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11075568	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11647408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1423780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1423781	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1862708	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4344745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8051747	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs876020	0.81[EUR][1000 genomes]
rs876021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs891209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs980783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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	esv34131	chr16:65137094-65379496	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv431508	chr16:65211408-65223172	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
3	nsv431509	chr16:65211408-65302840	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv431510	chr16:65213149-65223172	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
5	nsv431511	chr16:65213149-65252673	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	nsv431512	chr16:65213406-65234631	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1423785	CDH16	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65215000-65219200	Weak transcription	Brain Angular Gyrus	brain
2	chr16:65218000-65219800	Enhancers	Ovary	ovary
3	chr16:65218400-65219600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr16:65218400-65219600	Enhancers	Fetal Muscle Leg	muscle
5	chr16:65219000-65219400	Enhancers	Fetal Stomach	stomach
6	chr16:65219000-65219600	Enhancers	Colon Smooth Muscle	Colon
7	chr16:65219000-65219600	Enhancers	Right Atrium	heart

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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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