Variant report

Variant	rs4889006
Chromosome Location	chr16:79678349-79678350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10514466	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11150182	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11150185	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11150186	0.91[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs12932212	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12935094	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1424235	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2348181	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4889005	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6564685	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7204271	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8043576	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8055105	0.95[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv833295	chr16:79568878-79726768	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889006	ZNRF1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79666400-79682200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:79674400-79686400	Weak transcription	Fetal Thymus	thymus
3	chr16:79674800-79681600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr16:79675000-79678400	Weak transcription	HMEC	breast
5	chr16:79675200-79678600	Weak transcription	HSMM	muscle
6	chr16:79675200-79679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:79675200-79679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:79675200-79679200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:79675200-79679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr16:79675200-79685200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr16:79675400-79678800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:79675400-79685200	Weak transcription	Fetal Muscle Leg	muscle
13	chr16:79675600-79678600	Weak transcription	HSMMtube	muscle
14	chr16:79675600-79679800	Weak transcription	Fetal Lung	lung
15	chr16:79676400-79687800	Weak transcription	Fetal Kidney	kidney
16	chr16:79677600-79679000	Enhancers	NHEK	skin
17	chr16:79677600-79679400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:79677800-79679400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:79678200-79681600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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