Variant report

Variant	rs1524509
Chromosome Location	chr3:179688418-179688419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12492673	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12495455	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629537	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630104	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12631023	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635390	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635425	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060574	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13090261	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13096920	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13100713	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6787514	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6799006	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv33250	chr3:179688399-179688785	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179686000-179691400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:179686400-179689400	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr3:179686400-179691800	Weak transcription	Osteobl	bone
4	chr3:179686600-179688800	Enhancers	Fetal Brain Male	brain
5	chr3:179686800-179692000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:179686800-179692200	Active TSS	Brain Substantia Nigra	brain
7	chr3:179687000-179689400	Active TSS	Brain Cingulate Gyrus	brain
8	chr3:179687400-179692200	Active TSS	Brain Anterior Caudate	brain
9	chr3:179687800-179691000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:179688000-179688800	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr3:179688000-179688800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:179688000-179688800	Enhancers	Fetal Thymus	thymus
13	chr3:179688000-179688800	Enhancers	Thymus	Thymus
14	chr3:179688200-179688600	Active TSS	GM12878-XiMat	blood
15	chr3:179688200-179689000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:179688400-179690600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:179688400-179690800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:179688400-179692200	Active TSS	Brain Hippocampus Middle	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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