Variant report

Variant	rs12239225
Chromosome Location	chr1:166115389-166115390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10918343	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10918346	0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12060595	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs12070881	0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12239227	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57918730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61339873	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034656	0.87[AMR][1000 genomes]
rs73041247	0.87[AMR][1000 genomes]
rs74118994	0.85[AMR][1000 genomes]
rs9651029	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9651038	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3332610	chr1:166111288-166282689	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166106200-166119000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:166106600-166123200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:166109200-166119000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:166111200-166116400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:166113400-166122600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:166114200-166115400	Enhancers	NH-A	brain
7	chr1:166114600-166115800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr1:166114800-166120800	Weak transcription	Psoas Muscle	Psoas
9	chr1:166115000-166122600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:166115200-166115400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:166115200-166115800	Enhancers	Rectal Smooth Muscle	rectum

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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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