Variant report

Variant	rs17558139
Chromosome Location	chr14:70329553-70329554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11847221	0.94[ASN][1000 genomes]
rs17107367	0.94[ASN][1000 genomes]
rs1887146	0.90[ASN][1000 genomes]
rs1887147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1887148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952199	0.90[ASN][1000 genomes]
rs1952200	0.89[ASN][1000 genomes]
rs1958077	0.91[ASN][1000 genomes]
rs55749604	0.91[ASN][1000 genomes]
rs56222421	0.87[ASN][1000 genomes]
rs56403048	0.94[ASN][1000 genomes]
rs66954838	0.95[ASN][1000 genomes]
rs7147790	0.89[ASN][1000 genomes]
rs7155074	0.92[ASN][1000 genomes]
rs7156472	0.91[ASN][1000 genomes]
rs749397	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17558139	SLC8A3	cis	parietal	SCAN
rs17558139	TTC9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70328400-70332600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:70329200-70329800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr14:70329200-70330400	Enhancers	Liver	Liver
4	chr14:70329200-70330600	Enhancers	HepG2	liver
5	chr14:70329400-70340600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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