Variant report

Variant	rs3020449
Chromosome Location	chr14:64773392-64773393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10143616	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17101765	0.87[GIH][hapmap]
rs2978381	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2987969	0.82[CEU][hapmap]
rs2987983	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3020444	0.89[GIH][hapmap]
rs3020450	0.89[GIH][hapmap]
rs6573553	0.86[GIH][hapmap];0.80[JPT][hapmap]

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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1307	chr14:64742037-64787315	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3020449	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs3020449	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs3020449	MTHFD1	cis	cerebellum	SCAN
rs3020449	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs3020449	MTHFD1	cis	parietal	SCAN
rs3020449	SYNE2	cis	multi-tissue	Pritchard
rs3020449	SLC38A6	cis	cerebellum	SCAN
rs3020449	KCNH5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64772600-64773600	Enhancers	HepG2	liver

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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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