Variant report

Variant	rs13135838
Chromosome Location	chr4:175354852-175354853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11728322	0.93[AFR][1000 genomes]
rs11735634	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17052159	0.93[AFR][1000 genomes]
rs17052161	0.86[AFR][1000 genomes]
rs17060554	1.00[YRI][hapmap]
rs2195039	0.93[AFR][1000 genomes]
rs34674779	0.86[AFR][1000 genomes]
rs35539859	0.86[AFR][1000 genomes]
rs35706347	0.86[AFR][1000 genomes]
rs35931018	0.86[AFR][1000 genomes]
rs36112171	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs5012181	0.93[AFR][1000 genomes]
rs59300323	0.86[AFR][1000 genomes]
rs62337115	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62337116	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62337142	0.93[AFR][1000 genomes]
rs6827776	0.86[AFR][1000 genomes]
rs7666264	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][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	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13135838	VEGFC	cis	cerebellum	SCAN
rs13135838	SPCS3	cis	parietal	SCAN
rs13135838	HPGD	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175349000-175355200	Weak transcription	Placenta	Placenta
2	chr4:175350000-175358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:175351000-175355200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:175352000-175357200	Weak transcription	A549	lung

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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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