Variant report

Variant	rs12990539
Chromosome Location	chr2:145822058-145822059
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10496972	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10928240	0.82[ASN][1000 genomes]
rs12616953	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12618061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691705	0.81[ASN][1000 genomes]
rs12990953	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13028626	0.86[ASN][1000 genomes]
rs13033869	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16824386	1.00[MEX][hapmap];0.95[MKK][hapmap]
rs16824481	0.84[EUR][1000 genomes]
rs1830319	0.86[ASN][1000 genomes]
rs1830321	0.81[ASN][1000 genomes]
rs1852684	0.81[ASN][1000 genomes]
rs2381685	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2381686	0.86[ASN][1000 genomes]
rs2381687	0.82[ASN][1000 genomes]
rs34409381	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4662233	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4662413	0.87[AMR][1000 genomes]
rs4662414	0.86[ASN][1000 genomes]
rs6725803	0.81[ASN][1000 genomes]
rs67431032	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7561039	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834398	chr2:145659419-145830156	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv431768	chr2:145741527-145981491	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145819200-145826600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:145821400-145823400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:145821400-145825400	Enhancers	Fetal Lung	lung
4	chr2:145821400-145827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:145821600-145823400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:145821800-145822200	Weak transcription	Ovary	ovary
7	chr2:145821800-145823400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:145821800-145823400	Weak transcription	Brain Anterior Caudate	brain
9	chr2:145821800-145823600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:145821800-145823600	Enhancers	Osteobl	bone
11	chr2:145822000-145823200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:145822000-145823200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:145822000-145825800	Enhancers	NHDF-Ad	bronchial

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