Variant report

Variant	rs990357
Chromosome Location	chr9:3125198-3125199
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10115821	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10511443	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11794149	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13291256	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1412695	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1412696	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1412697	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34159830	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34920816	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4740714	0.83[EUR][1000 genomes]
rs4740716	0.87[EUR][1000 genomes]
rs62532606	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6476283	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6476300	0.86[EUR][1000 genomes]
rs7020981	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7020987	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7021228	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022143	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7031732	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032007	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7032582	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7035531	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7039721	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7040290	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7853519	1.00[JPT][hapmap]
rs7854436	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7857427	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7858703	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7867500	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7868524	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7874654	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs928449	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs928450	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892085	chr9:2937654-3215842	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831494	chr9:3007268-3172056	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv892087	chr9:3014702-3153178	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv892088	chr9:3019383-3215842	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1015601	chr9:3095312-3150287	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv1029974	chr9:3107487-3146891	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
11	nsv1024242	chr9:3112966-3156620	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs990357	VLDLR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3124000-3125400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:3124000-3125400	Active TSS	Stomach Smooth Muscle	stomach
3	chr9:3124200-3125200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:3124200-3125400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:3124400-3125600	Weak transcription	Fetal Lung	lung
6	chr9:3124800-3125800	Weak transcription	Primary hematopoietic stem cells	blood

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