Variant report

Variant	rs9862546
Chromosome Location	chr3:143353266-143353267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11707596	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11714312	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715331	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11719597	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16853938	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28882205	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58204786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59945058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60557516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810333	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9810826	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9811274	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs9863063	0.95[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9879940	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143324400-143353800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:143328200-143376200	Weak transcription	Ovary	ovary
3	chr3:143337400-143354200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:143339200-143355200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:143346400-143363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:143346600-143355600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:143348200-143355400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:143351600-143369800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:143352000-143355600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:143352600-143353800	Weak transcription	Esophagus	oesophagus
11	chr3:143352800-143354400	Enhancers	Duodenum Mucosa	Duodenum
12	chr3:143353000-143353800	Weak transcription	Small Intestine	intestine
13	chr3:143353200-143354400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte 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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