Variant report

Variant	rs17613247
Chromosome Location	chr7:126328230-126328231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10225708	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10240139	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1345210	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361991	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17683462	0.84[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17683715	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs17691394	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28693977	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv889187	chr7:126219766-126478190	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1032108	chr7:126278349-126362592	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17613247	TMEM209	cis	parietal	SCAN
rs17613247	CPA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126321800-126328800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr7:126323600-126328600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:126326000-126331200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:126326600-126330200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:126326800-126330200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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