Variant report

Variant	rs521890
Chromosome Location	chr15:41473143-41473144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10518717	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10851403	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070328	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11852419	0.93[EUR][1000 genomes]
rs11854081	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11854632	1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11855854	0.89[EUR][1000 genomes]
rs11856169	0.81[EUR][1000 genomes]
rs13313520	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13329235	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329579	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs17730589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17730888	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	1.00[ASN][1000 genomes]
rs2118740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2448402	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs28377562	1.00[ASN][1000 genomes]
rs28382348	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28463309	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28477406	1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493087	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493702	1.00[CHB][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs28516832	0.81[EUR][1000 genomes]
rs28524914	0.91[EUR][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28538451	0.93[EUR][1000 genomes]
rs28554139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs28557159	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	1.00[ASN][1000 genomes]
rs28661013	1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28897479	1.00[ASN][1000 genomes]
rs3204853	1.00[ASN][1000 genomes]
rs513280	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533210	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56400990	1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs691011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691629	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs691906	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7168431	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7169543	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7181982	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72737786	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737792	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737793	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739630	1.00[ASN][1000 genomes]
rs8023530	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8037574	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8038983	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043237	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs521890	NDUFAF1	cis	parietal	SCAN
rs521890	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs521890	GPR176	cis	parietal	SCAN
rs521890	NDUFAF1	cis	lymphoblastoid	seeQTL
rs521890	NDUFAF1	cis	multi-tissue	Pritchard
rs521890	NUSAP1	cis	cerebellum	SCAN
rs521890	GPR176	cis	cerebellum	SCAN
rs521890	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs521890	NUSAP1	cis	parietal	SCAN
rs521890	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs521890	NDUFAF1	cis	cerebellum	SCAN
rs521890	NDUFAF1	cis	Thyroid	GTEx
rs521890	BUB1B	cis	parietal	SCAN
rs521890	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs521890	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs521890	NDUFAF1	cis	Muscle Skeletal	GTEx
rs521890	NDUFAF1	cis	Whole Blood	GTEx
rs521890	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs521890	OIP5-AS1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41472200-41473400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:41472400-41473200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr15:41472600-41473200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:41472800-41473200	Flanking Active TSS	Osteobl	bone
5	chr15:41472800-41476000	Weak transcription	NH-A	brain
6	chr15:41472800-41476200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:41473000-41474400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:41473000-41474400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:41473000-41476000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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