Variant report

Variant	rs1520487
Chromosome Location	chr3:46676035-46676036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11130098	0.92[ASN][1000 genomes]
rs11130100	0.98[ASN][1000 genomes]
rs11709020	0.96[ASN][1000 genomes]
rs11709936	0.97[ASN][1000 genomes]
rs11710264	0.92[ASN][1000 genomes]
rs12330414	0.92[ASN][1000 genomes]
rs13319345	0.87[ASN][1000 genomes]
rs2385858	0.92[ASN][1000 genomes]
rs2891885	0.87[ASN][1000 genomes]
rs3796371	0.97[ASN][1000 genomes]
rs6442010	0.96[ASN][1000 genomes]
rs6805749	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610008	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7643859	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876738	chr3:46639048-46680063	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46672000-46677200	Weak transcription	Fetal Brain Female	brain
2	chr3:46672000-46677600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:46672000-46681600	Weak transcription	Left Ventricle	heart
4	chr3:46672400-46676400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:46674800-46676400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:46675000-46676400	Weak transcription	Liver	Liver
7	chr3:46675200-46677600	Enhancers	Spleen	Spleen
8	chr3:46675200-46677600	Enhancers	Dnd41	blood
9	chr3:46675400-46676800	Enhancers	Primary T cells from cord blood	blood
10	chr3:46675400-46677000	Enhancers	Fetal Thymus	thymus
11	chr3:46675600-46676400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:46675600-46688000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:46675800-46676600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr3:46675800-46676600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr3:46676000-46676600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr3:46676000-46676600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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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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