Variant report

Variant	rs2176998
Chromosome Location	chr15:41420807-41420808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1001341	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1009913	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs11070315	0.96[CEU][hapmap]
rs11853192	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11854472	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855248	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs11855797	0.89[ASN][1000 genomes]
rs11856572	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856577	0.83[EUR][1000 genomes]
rs11856848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11858678	0.82[MEX][hapmap]
rs1678750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1717200	0.90[EUR][1000 genomes]
rs1869907	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs1962410	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1983400	0.91[ASN][1000 genomes]
rs2306083	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412601	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28409432	0.93[ASN][1000 genomes]
rs28455998	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28473405	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs28510775	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28516683	0.93[ASN][1000 genomes]
rs28581803	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28613002	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28664602	0.87[AFR][1000 genomes]
rs28688742	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28729675	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28828670	0.85[ASN][1000 genomes]
rs28866311	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899002	0.96[CEU][hapmap]
rs2925343	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2925345	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2927061	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2927062	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2928148	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928156	0.91[ASN][1000 genomes]
rs2947493	0.91[ASN][1000 genomes]
rs2947494	0.91[ASN][1000 genomes]
rs3100807	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs3101436	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs3101442	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3214068	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs36046988	0.91[ASN][1000 genomes]
rs3900905	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4592624	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs476633	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs516156	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs544744	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs561301	0.93[ASN][1000 genomes]
rs57393155	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6492983	0.93[ASN][1000 genomes]
rs66818965	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690733	0.82[MEX][hapmap]
rs691672	0.91[ASN][1000 genomes]
rs691830	0.91[EUR][1000 genomes]
rs692153	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs692155	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[EUR][1000 genomes]
rs692195	0.93[ASN][1000 genomes]
rs7162992	0.80[EUR][1000 genomes]
rs7169375	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs7173841	0.93[ASN][1000 genomes]
rs7179681	0.86[EUR][1000 genomes]
rs7180853	0.93[ASN][1000 genomes]
rs7181816	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72737704	0.82[EUR][1000 genomes]
rs8023345	0.83[EUR][1000 genomes]
rs8027932	0.92[ASN][1000 genomes]
rs8033435	0.93[ASN][1000 genomes]
rs8037837	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8042088	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs909024	0.83[CHB][hapmap]
rs9796	0.92[CEU][hapmap]
rs9888710	0.93[ASN][1000 genomes]
rs9888718	0.93[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2176998	BUB1B	cis	parietal	SCAN
rs2176998	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs2176998	NDUFAF1	cis	parietal	SCAN
rs2176998	NDUFAF1	cis	lymphoblastoid	seeQTL
rs2176998	CASC5	cis	cerebellum	SCAN
rs2176998	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs2176998	NDUFAF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41409600-41427600	Weak transcription	Hela-S3	cervix
2	chr15:41418400-41423200	Weak transcription	Stomach Mucosa	stomach
3	chr15:41419000-41421600	Enhancers	HepG2	liver
4	chr15:41419600-41421800	Enhancers	Liver	Liver
5	chr15:41420200-41421200	Enhancers	Fetal Intestine Small	intestine
6	chr15:41420600-41421000	Flanking Active TSS	A549	lung
7	chr15:41420600-41421400	Enhancers	Fetal Intestine Large	intestine

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