Variant report

Variant	rs539299
Chromosome Location	chr10:89957033-89957034
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs473875	0.84[ASN][1000 genomes]
rs475618	0.88[ASN][1000 genomes]
rs481840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs490265	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs501751	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs505384	0.90[EUR][1000 genomes]
rs510727	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536243	0.91[ASN][1000 genomes]
rs538292	0.90[EUR][1000 genomes]
rs575865	0.81[EUR][1000 genomes]
rs577880	1.00[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs640906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642864	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9804295	0.98[AMR][1000 genomes];0.82[EUR][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	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89951000-89965600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr10:89954200-89957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:89954400-89957800	Weak transcription	NHEK	skin
4	chr10:89954800-89957600	Weak transcription	HMEC	breast
5	chr10:89955200-89960000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:89955400-89959200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr10:89955400-89960400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr10:89955400-89962400	Weak transcription	Left Ventricle	heart
9	chr10:89955400-89963800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:89955400-89965000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:89955400-89998000	Weak transcription	Aorta	Aorta
12	chr10:89956200-89959600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:89956400-89959200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:89956400-89960000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:89956600-89960400	Weak transcription	Fetal Muscle Leg	muscle

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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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