Variant report

Variant	rs3820041
Chromosome Location	chr1:86919011-86919012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12023799	0.81[ASN][1000 genomes]
rs12747430	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36096788	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737671	0.85[ASN][1000 genomes]
rs3765984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765987	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820038	0.93[ASN][1000 genomes]
rs4656103	1.00[ASN][1000 genomes]
rs55812833	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55825812	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55857117	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56187142	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5744303	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs5744321	1.00[AFR][1000 genomes]
rs5744349	1.00[AFR][1000 genomes]
rs57955693	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58658794	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59775624	0.90[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	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv521366	chr1:86916767-86922161	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:86897200-86922800	Strong transcription	HMEC	breast
3	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus
4	chr1:86914600-86930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:86915200-86920000	Strong transcription	NHEK	skin
6	chr1:86915600-86919400	Weak transcription	K562	blood
7	chr1:86916400-86921600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:86917000-86930600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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