Variant report

Variant	rs2712593
Chromosome Location	chr12:46010428-46010429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2544081	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712591	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712592	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs2712594	1.00[CEU][hapmap]
rs2712596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2712597	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2712598	1.00[CEU][hapmap]
rs2712599	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs2712600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2712601	1.00[CEU][hapmap]
rs2712602	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58817739	1.00[ASN][1000 genomes]
rs7958336	0.89[JPT][hapmap]

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	nsv832395	chr12:45841765-46039297	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2751099	chr12:45960118-46043633	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv983462	chr12:46008670-46015543	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2712593	SLC48A1	cis	parietal	SCAN
rs2712593	PPHLN1	cis	cerebellum	SCAN
rs2712593	P2RY2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46005400-46011800	Weak transcription	Right Atrium	heart
2	chr12:46007600-46010600	Enhancers	Hela-S3	cervix
3	chr12:46009600-46010600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:46009600-46010600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:46010000-46011000	Weak transcription	HUVEC	blood vessel

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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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