Variant report

Variant	rs1609789
Chromosome Location	chr3:179587667-179587668
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:19)

rs_ID	r²[population]
rs10937012	0.93[CEU][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11713949	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12107337	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12492963	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1567623	0.92[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1609788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177592	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302743	0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2339914	0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2339916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35504390	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774239	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3774240	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4854953	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55664665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6443674	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6443676	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6769641	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7616060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179533800-179605000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:179537800-179599400	Weak transcription	Brain Anterior Caudate	brain
3	chr3:179554000-179590400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:179559600-179589400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:179564200-179606000	Strong transcription	Dnd41	blood
6	chr3:179571400-179596800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:179575200-179591200	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:179577000-179588000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:179580200-179598600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:179586800-179588000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:179586800-179591200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:179587000-179588400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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