Variant report

Variant	rs17179740
Chromosome Location	chr14:64756751-64756752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12101211	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12323665	0.84[ASN][1000 genomes]
rs17101765	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2987983	0.89[GIH][hapmap]
rs3020444	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs3020450	0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3783736	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4986938	0.81[CEU][hapmap]
rs6573552	0.85[ASN][1000 genomes]
rs6573553	0.88[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7154455	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs8011682	0.93[ASN][1000 genomes]
rs8020356	0.86[ASN][1000 genomes]
rs960070	0.80[CHB][hapmap];0.85[JPT][hapmap];0.84[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17179740	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs17179740	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs17179740	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs17179740	KCNH5	cis	parietal	SCAN
rs17179740	SYNE2	cis	multi-tissue	Pritchard
rs17179740	MTHFD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64727600-64757600	Weak transcription	Ovary	ovary
2	chr14:64735400-64757200	Weak transcription	Thymus	Thymus
3	chr14:64755800-64757000	Enhancers	Adipose Nuclei	Adipose
4	chr14:64756600-64757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:64756600-64760200	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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