Variant report

Variant	rs4889002
Chromosome Location	chr16:79661912-79661913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10871373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11150179	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11859272	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs250141	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs250142	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs250143	0.90[EUR][1000 genomes]
rs4888038	0.86[EUR][1000 genomes]
rs6564682	0.89[AMR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4889002	GAN	cis	cerebellum	SCAN
rs4889002	ZNRF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79657600-79662000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr16:79660400-79662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:79660800-79662000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr16:79661400-79663400	Enhancers	HMEC	breast
5	chr16:79661600-79663200	Enhancers	NH-A	brain
6	chr16:79661600-79663200	Enhancers	Osteobl	bone
7	chr16:79661800-79663000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr16:79661800-79663000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:79661800-79663000	Enhancers	NHEK	skin
10	chr16:79661800-79663200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:79661800-79663200	Enhancers	Primary hematopoietic stem cells	blood
12	chr16:79661800-79663200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr16:79661800-79663200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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