Variant report

Variant	rs28866311
Chromosome Location	chr15:41442195-41442196
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1009913	0.86[EUR][1000 genomes]
rs11853192	0.85[ASN][1000 genomes]
rs11854472	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11855797	0.94[ASN][1000 genomes]
rs11856572	0.86[EUR][1000 genomes]
rs11856577	0.82[EUR][1000 genomes]
rs11856848	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678750	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1717200	0.90[EUR][1000 genomes]
rs1962410	0.83[EUR][1000 genomes]
rs1983400	0.86[ASN][1000 genomes]
rs2176998	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306083	0.85[EUR][1000 genomes]
rs2412601	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28409432	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs28455998	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28510775	0.85[ASN][1000 genomes]
rs28516683	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs28581803	0.85[EUR][1000 genomes]
rs28613002	0.87[ASN][1000 genomes]
rs28688742	0.87[ASN][1000 genomes]
rs28729675	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28828670	0.89[ASN][1000 genomes]
rs2928141	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2928148	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2928156	0.96[ASN][1000 genomes]
rs2947493	0.86[ASN][1000 genomes]
rs2947494	0.86[ASN][1000 genomes]
rs3101442	0.86[EUR][1000 genomes]
rs36046988	0.85[ASN][1000 genomes]
rs4592624	0.88[ASN][1000 genomes]
rs476633	0.88[ASN][1000 genomes]
rs516156	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544744	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561301	0.99[ASN][1000 genomes]
rs57393155	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492983	0.99[ASN][1000 genomes]
rs66818965	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs691672	0.98[ASN][1000 genomes]
rs691830	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs692153	0.98[ASN][1000 genomes]
rs692155	0.91[EUR][1000 genomes]
rs692195	0.99[ASN][1000 genomes]
rs7173841	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7179681	0.84[EUR][1000 genomes]
rs7180853	0.99[ASN][1000 genomes]
rs7181816	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8027932	0.98[ASN][1000 genomes]
rs8033435	0.99[ASN][1000 genomes]
rs8037837	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8042088	0.85[EUR][1000 genomes]
rs9888710	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9888718	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised 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	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv904109	chr15:41410705-41481254	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv10980	chr15:41423683-41445889	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28866311	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28866311	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28866311	NDUFAF1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41440800-41442600	Weak transcription	NHLF	lung
2	chr15:41441400-41443000	Enhancers	Liver	Liver
3	chr15:41441400-41443600	Enhancers	NHEK	skin
4	chr15:41441600-41443600	Enhancers	Hela-S3	cervix
5	chr15:41441800-41442800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr15:41441800-41443000	Enhancers	HepG2	liver
7	chr15:41441800-41443200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:41441800-41443200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:41442000-41443000	Enhancers	Fetal Kidney	kidney

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