Variant report

Variant	rs4854755
Chromosome Location	chr3:133452671-133452672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10049093	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10935081	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10935083	0.91[ASN][1000 genomes]
rs11715340	0.87[ASN][1000 genomes]
rs11717407	0.88[ASN][1000 genomes]
rs16840692	0.84[ASN][1000 genomes]
rs16840699	0.88[ASN][1000 genomes]
rs16840751	0.89[ASN][1000 genomes]
rs16840812	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1799852	0.82[JPT][hapmap]
rs4241356	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4428180	0.87[ASW][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs4532136	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4582061	0.88[ASN][1000 genomes]
rs4854595	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4854748	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4854749	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4854750	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4854752	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4854754	0.89[ASN][1000 genomes]
rs4854757	0.91[ASN][1000 genomes]
rs6801244	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8177181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8177184	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8177185	0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8177186	0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8177203	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs8177215	0.82[JPT][hapmap]
rs9714237	0.84[ASN][1000 genomes]
rs9847885	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4854755	NCK1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133442000-133453200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:133450000-133453400	Enhancers	Pancreas	Pancrea
3	chr3:133451400-133453600	Flanking Active TSS	Liver	Liver
4	chr3:133452200-133452800	Weak transcription	Gastric	stomach
5	chr3:133452400-133453400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:133452600-133454000	Enhancers	HepG2	liver

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