Variant report

Variant	rs12899879
Chromosome Location	chr15:58591415-58591416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12903590	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910051	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1711037	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1711041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71478659	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7179728	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs938507	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv904266	chr15:58580921-58689187	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58587400-58598800	Weak transcription	Fetal Kidney	kidney
2	chr15:58589600-58592000	ZNF genes & repeats	GM12878-XiMat	blood
3	chr15:58590000-58592000	Enhancers	Fetal Thymus	thymus
4	chr15:58590200-58591600	Enhancers	Thymus	Thymus
5	chr15:58590200-58602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:58590800-58591600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:58590800-58591600	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr15:58590800-58591800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:58590800-58591800	Enhancers	NHDF-Ad	bronchial
10	chr15:58590800-58592200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:58590800-58592800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:58591000-58592000	Enhancers	Adipose Nuclei	Adipose
13	chr15:58591000-58592200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:58591000-58592200	Enhancers	Osteobl	bone
15	chr15:58591000-58594600	Weak transcription	Liver	Liver
16	chr15:58591200-58592000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:58591200-58592000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:58591200-58592000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:58591200-58592000	Enhancers	Fetal Muscle Leg	muscle
20	chr15:58591400-58591600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:58591400-58591800	Enhancers	Lung	lung
22	chr15:58591400-58591800	Enhancers	NH-A	brain
23	chr15:58591400-58592000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:58591400-58592000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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