Variant report

Variant	rs17769783
Chromosome Location	chr7:52654649-52654650
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17152698	0.89[ASN][1000 genomes]
rs17769977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17831541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120104	0.89[ASN][1000 genomes]
rs73120105	0.89[ASN][1000 genomes]
rs73120117	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	nsv888026	chr7:52588348-53013671	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv888027	chr7:52588348-53190508	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17769783	PTPRN2	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:52651200-52655800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr7:52654200-52656000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:52654400-52655000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:52654600-52654800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr7:52654600-52655400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:52654600-52656400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:52654600-52656600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:52654600-52657600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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