Variant report

Variant	rs2852723
Chromosome Location	chr1:159073725-159073726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16841642	0.82[GIH][hapmap]
rs1894043	1.00[ASN][1000 genomes]
rs1935067	0.82[GIH][hapmap]
rs2078723	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298803	0.82[GIH][hapmap]
rs2518562	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2518563	0.90[ASN][1000 genomes]
rs2518564	0.90[ASN][1000 genomes]
rs2518565	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570916	0.81[CHD][hapmap];0.85[MEX][hapmap]
rs2814757	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814759	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814760	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814764	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs855866	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs855867	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs855871	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2852723	AIM2	cis	lymphoblastoid	seeQTL
rs2852723	S100A7A	cis	parietal	SCAN
rs2852723	CCDC19	cis	cerebellum	SCAN
rs2852723	PMF1	cis	parietal	SCAN
rs2852723	PHGDH	trans	lymphoblastoid	seeQTL
rs2852723	FCRL4	cis	cerebellum	SCAN
rs2852723	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs2852723	PEA15	cis	cerebellum	SCAN
rs2852723	DPM3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159072200-159075000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:159073200-159075400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:159073400-159073800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr1:159073600-159074200	Enhancers	Adipose Derived Mesenchymal Stem Cell 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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