Variant report

Variant	rs11869749
Chromosome Location	chr17:50305523-50305524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10514999	0.81[EUR][1000 genomes]
rs11867439	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1825733	0.83[EUR][1000 genomes]
rs1825734	0.81[EUR][1000 genomes]
rs1872724	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504760	0.81[EUR][1000 genomes]
rs6504763	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214564	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9303597	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902514	0.86[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	nsv492317	chr17:50067819-50774475	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1064193	chr17:50270352-50320667	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1064285	chr17:50290372-50507829	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv543385	chr17:50290372-50507829	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11869749	UBE2Z	cis	parietal	SCAN
rs11869749	PNPO	cis	parietal	SCAN
rs11869749	NFE2L1	cis	parietal	SCAN
rs11869749	PDK2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:50304600-50306600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:50304600-50306600	Enhancers	HMEC	breast
3	chr17:50304800-50306600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:50304800-50306800	Enhancers	Brain Substantia Nigra	brain
5	chr17:50305000-50306400	Enhancers	NHEK	skin
6	chr17:50305200-50305600	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr17:50305400-50305600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:50305400-50305800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
9	chr17:50305400-50306600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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