Variant report

Variant	rs16998675
Chromosome Location	chr4:147138193-147138194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10006650	0.91[ASN][1000 genomes]
rs10014590	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12374409	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998674	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021239	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17021241	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17021249	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021264	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17335848	0.80[YRI][hapmap];0.83[AFR][1000 genomes]
rs28605093	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3860098	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55762555	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844150	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56331233	0.99[ASN][1000 genomes]
rs60241278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60701696	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326849	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62326850	0.99[ASN][1000 genomes]
rs62326851	0.99[ASN][1000 genomes]
rs6813969	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6816198	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835911	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6838174	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6843421	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6848943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849193	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854775	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72727960	0.99[ASN][1000 genomes]
rs9993525	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16998675	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs16998675	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs16998675	RP11-6L6.2	cis	lung	GTEx
rs16998675	LSM6	cis	cerebellum	SCAN
rs16998675	LSM6	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147114000-147144800	Weak transcription	Gastric	stomach
2	chr4:147136600-147144400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:147138000-147138200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:147138000-147138400	Enhancers	Lung	lung

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