Variant report

Variant	rs319870
Chromosome Location	chr7:78229176-78229177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11765998	0.86[AFR][1000 genomes]
rs11970969	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs17439220	0.95[CEU][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2192659	0.82[CEU][hapmap]
rs319871	0.86[CEU][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs319872	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs319873	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs319874	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs319875	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468650	0.86[AFR][1000 genomes]
rs62468651	0.86[AFR][1000 genomes]
rs62468652	0.86[AFR][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	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
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs319870	PTPN12	cis	cerebellum	SCAN
rs319870	LOC100133091	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78219000-78258600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:78222400-78233600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:78223600-78232400	Weak transcription	Brain Anterior Caudate	brain
4	chr7:78229000-78229200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:78229000-78229400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:78229000-78229400	Enhancers	HepG2	liver
7	chr7:78229000-78229600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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

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