Variant report

Variant	rs56005976
Chromosome Location	chr3:115771488-115771489
allele	A/C/T
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:13)

rs_ID	r²[population]
rs13324008	0.87[AMR][1000 genomes]
rs1343647	0.85[AMR][1000 genomes]
rs1920362	0.85[AMR][1000 genomes]
rs1920377	0.85[AMR][1000 genomes]
rs4476499	0.85[AMR][1000 genomes]
rs56142426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58398368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59057906	0.85[AMR][1000 genomes]
rs73858507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73858510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73858512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827294	0.87[AMR][1000 genomes]
rs9832312	0.87[AMR][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	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1001538	chr3:115746561-115791116	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115758000-115772800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:115759000-115778200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:115766000-115774000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:115766000-115775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:115766200-115794200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:115770000-115771600	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:115770400-115775800	Weak transcription	HMEC	breast
8	chr3:115770400-115777000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:115770600-115774400	Weak transcription	GM12878-XiMat	blood
10	chr3:115770800-115772800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:115771000-115773800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:115771400-115771600	Weak transcription	Brain Substantia Nigra	brain

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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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