Variant report

Variant	rs2012593
Chromosome Location	chr7:78014174-78014175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12533999	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12536414	0.81[LWK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs12539788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs17350367	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17350535	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17415846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34992850	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55761537	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55824893	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59825513	0.82[AMR][1000 genomes]
rs62461472	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62461545	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62461546	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468259	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62468766	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7782154	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810316	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs881447	0.83[GIH][hapmap];0.85[AMR][1000 genomes];0.85[EUR][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	nsv607654	chr7:77537964-78014329	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1033518	chr7:78013657-78038797	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2012593	PTPN12	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78010000-78024600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:78012200-78018600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:78013000-78014200	Weak transcription	Brain Substantia Nigra	brain

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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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