Variant report

Variant	rs3902960
Chromosome Location	chr2:127988242-127988243
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10209678	0.81[ASN][1000 genomes]
rs10928761	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12463909	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465955	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12469035	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12623948	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12692064	0.81[ASN][1000 genomes]
rs1566822	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2174270	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2896888	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35328149	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150407	0.92[EUR][1000 genomes]
rs4497825	0.83[EUR][1000 genomes]
rs4560059	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4580338	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4662710	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4662711	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4662712	0.88[EUR][1000 genomes]
rs4662717	0.94[EUR][1000 genomes]
rs55905117	0.88[EUR][1000 genomes]
rs58475809	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6430931	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6712213	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6712446	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6712551	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731176	0.83[EUR][1000 genomes]
rs71414745	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7568261	0.83[EUR][1000 genomes]
rs7585198	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7591760	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9636235	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9636236	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3902960	AC068282.3	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127984600-128012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:127988200-127989800	Enhancers	Liver	Liver
3	chr2:127988200-127990200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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