Variant report

Variant	rs4454988
Chromosome Location	chr16:80006534-80006535
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80005070..80008604-chr16:80010257..80012761,6	K562	blood:
2	chr16:80005028..80007365-chr16:80012066..80013670,2	K562	blood:
3	chr16:79998134..80000055-chr16:80005510..80007697,2	MCF-7	breast:
4	chr16:79978107..79980812-chr16:80004750..80007386,2	K562	blood:
5	chr16:79870162..79872603-chr16:80005430..80007622,2	K562	blood:
6	chr16:80006211..80008346-chr16:80008458..80011318,2	K562	blood:
7	chr16:79998660..80002282-chr16:80003474..80007904,4	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11150233	0.83[ASN][1000 genomes]
rs11150235	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11862161	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12051447	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12051451	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34972526	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35226245	0.92[ASN][1000 genomes]
rs35651281	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36078655	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4146392	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4468637	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4513112	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4545829	0.99[ASN][1000 genomes]
rs4603570	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4606730	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5029357	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5029358	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5029360	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5029362	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5029363	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66539665	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7188398	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7188559	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8045969	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9941084	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9941093	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv573294	chr16:80005642-80131944	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4454988	VAT1L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80004000-80006600	Flanking Active TSS	K562	blood
2	chr16:80005800-80006600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr16:80005800-80006800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:80006000-80006600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:80006000-80006600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr16:80006000-80006600	Enhancers	HSMMtube	muscle
7	chr16:80006200-80006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:80006200-80006600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr16:80006200-80006600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:80006200-80006600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr16:80006200-80006600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr16:80006200-80006600	Enhancers	HSMM	muscle
13	chr16:80006400-80015000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links