Variant report

Variant	rs8053297
Chromosome Location	chr16:46876576-46876577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1009391	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10468399	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs11860484	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11861896	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11862073	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12934580	1.00[ASN][1000 genomes]
rs1641121	0.87[EUR][1000 genomes]
rs1641122	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651654	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs166161	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs16948661	0.93[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17189741	0.86[CEU][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs1869006	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2192644	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341041	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2341043	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36310	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs36471	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs36481	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40355	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs41187	0.81[TSI][hapmap]
rs4141491	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs415018	0.83[EUR][1000 genomes]
rs4246381	1.00[ASN][1000 genomes]
rs4401068	0.90[GIH][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.81[YRI][hapmap]
rs4966616	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4966706	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs4966708	1.00[GIH][hapmap];0.87[MKK][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs4966710	1.00[ASN][1000 genomes]
rs4966713	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4967576	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs4967621	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs56042735	1.00[ASN][1000 genomes]
rs57127559	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62057633	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	1.00[ASN][1000 genomes]
rs66804065	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67205347	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67211229	1.00[ASN][1000 genomes]
rs67369452	1.00[ASN][1000 genomes]
rs68162608	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs698418	0.82[EUR][1000 genomes]
rs700582	0.82[GIH][hapmap]
rs7187475	0.93[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7196375	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7197485	0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs7198951	0.84[EUR][1000 genomes]
rs72812428	1.00[ASN][1000 genomes]
rs734309	0.89[GIH][hapmap]
rs794279	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs8044443	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045353	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8051017	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8053137	1.00[ASN][1000 genomes]
rs8058734	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808432	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808434	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs808780	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs808783	0.86[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9328668	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv1067283	chr16:46801709-46885218	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv3351528	chr16:46853500-46877470	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8053297	LONP2	cis	cerebellum	SCAN
rs8053297	MYLK3	cis	cerebellum	SCAN
rs8053297	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs8053297	SHCBP1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46865600-46878200	Weak transcription	Right Atrium	heart
2	chr16:46875400-46880200	Weak transcription	HepG2	liver
3	chr16:46876400-46876600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links