Variant report

Variant	rs12072027
Chromosome Location	chr1:86062222-86062223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12061951	0.86[CEU][hapmap]
rs12239954	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1329961	0.92[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1576423	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6658857	0.82[EUR][1000 genomes]
rs6673340	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9651137	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9803850	0.92[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12072027	ITM2B	trans	lymphoblastoid	seeQTL
rs12072027	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86049000-86068400	Weak transcription	Psoas Muscle	Psoas
3	chr1:86051000-86062800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:86053800-86064600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:86053800-86071400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:86055000-86064800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:86055200-86064600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:86062200-86062400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:86062200-86063000	Enhancers	Fetal Lung	lung

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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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