Variant report

Variant	rs7206909
Chromosome Location	chr16:48236666-48236667
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10163354	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10163462	1.00[ASN][1000 genomes]
rs10221107	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs11076561	0.80[EUR][1000 genomes]
rs11076565	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs11552148	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs11861031	1.00[ASN][1000 genomes]
rs11861127	0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs11863133	0.93[ASN][1000 genomes]
rs11863233	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs11863236	0.85[CHD][hapmap];0.93[ASN][1000 genomes]
rs11863325	1.00[ASN][1000 genomes]
rs11866251	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11866312	0.93[ASN][1000 genomes]
rs11866529	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12103095	0.80[EUR][1000 genomes]
rs12149230	0.82[EUR][1000 genomes]
rs13330082	0.80[EUR][1000 genomes]
rs13331250	0.80[EUR][1000 genomes]
rs13336264	0.88[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13336771	0.80[EUR][1000 genomes]
rs1545942	0.88[CEU][hapmap]
rs16945916	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs16945917	1.00[ASN][1000 genomes]
rs16945919	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs16945972	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs16945974	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs16946038	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs16946039	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs17743256	1.00[ASN][1000 genomes]
rs1843647	0.80[EUR][1000 genomes]
rs28376623	0.93[ASN][1000 genomes]
rs28378550	0.81[EUR][1000 genomes]
rs28503414	0.93[ASN][1000 genomes]
rs28605399	0.85[ASN][1000 genomes]
rs28617382	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs28626252	0.93[ASN][1000 genomes]
rs28654935	0.93[ASN][1000 genomes]
rs28684834	0.93[ASN][1000 genomes]
rs28696036	0.93[ASN][1000 genomes]
rs28823370	0.80[EUR][1000 genomes]
rs34135802	0.80[EUR][1000 genomes]
rs41280939	1.00[ASN][1000 genomes]
rs4528570	0.80[EUR][1000 genomes]
rs5017203	0.93[ASN][1000 genomes]
rs57912486	1.00[ASN][1000 genomes]
rs58409512	0.86[EUR][1000 genomes]
rs59916796	0.80[EUR][1000 genomes]
rs60745528	0.81[EUR][1000 genomes]
rs60760669	0.81[EUR][1000 genomes]
rs62058521	1.00[ASN][1000 genomes]
rs62058522	1.00[ASN][1000 genomes]
rs62058526	1.00[ASN][1000 genomes]
rs62058528	1.00[ASN][1000 genomes]
rs6500339	0.92[ASN][1000 genomes]
rs6500385	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs7184831	1.00[ASN][1000 genomes]
rs7186777	0.81[EUR][1000 genomes]
rs7187233	0.94[CEU][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191844	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7196373	0.84[CEU][hapmap]
rs7203695	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs73540901	0.93[ASN][1000 genomes]
rs73542903	0.93[ASN][1000 genomes]
rs73542904	0.93[ASN][1000 genomes]
rs73546434	0.85[ASN][1000 genomes]
rs73546437	0.85[ASN][1000 genomes]
rs73546439	0.85[ASN][1000 genomes]
rs73562063	0.81[EUR][1000 genomes]
rs74018298	0.92[ASN][1000 genomes]
rs74018300	1.00[ASN][1000 genomes]
rs8043803	0.80[EUR][1000 genomes]
rs8045819	0.81[EUR][1000 genomes]
rs8046408	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs8046814	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047091	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047397	0.85[ASN][1000 genomes]
rs8048098	0.88[CEU][hapmap]
rs8050120	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051016	0.88[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8051186	0.81[EUR][1000 genomes]
rs8051205	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8051441	0.88[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap]
rs8054314	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.83[EUR][1000 genomes]
rs8055028	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs8055128	0.85[ASN][1000 genomes]
rs8056100	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs8056143	0.85[ASN][1000 genomes]
rs8056846	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs8057475	0.88[CEU][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8060696	0.85[ASN][1000 genomes]
rs8060722	0.85[ASN][1000 genomes]
rs8060780	0.80[EUR][1000 genomes]
rs8190	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.83[EUR][1000 genomes]
rs9302757	0.80[EUR][1000 genomes]
rs9302758	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap]
rs957881	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9925772	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs9925935	0.80[EUR][1000 genomes]
rs9931294	0.80[EUR][1000 genomes]
rs9932850	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9932964	0.80[EUR][1000 genomes]
rs9938003	0.80[EUR][1000 genomes]
rs9938523	0.85[EUR][1000 genomes]
rs9939742	1.00[CHD][hapmap]
rs9940038	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs9941123	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7206909	LONP2	cis	parietal	SCAN
rs7206909	LONP2	Cis_1M	lymphoblastoid	RTeQTL
rs7206909	LONP2	cis	cerebellum	SCAN
rs7206909	LONPL	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48230200-48240400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:48234400-48237400	Weak transcription	Fetal Intestine Small	intestine
3	chr16:48235400-48236800	Enhancers	Adipose Nuclei	Adipose
4	chr16:48235400-48237200	Enhancers	Pancreas	Pancrea
5	chr16:48235400-48238000	Enhancers	HepG2	liver
6	chr16:48235400-48238800	Enhancers	Liver	Liver
7	chr16:48235600-48237000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr16:48236000-48237400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr16:48236000-48238000	Weak transcription	Stomach Mucosa	stomach
10	chr16:48236000-48238400	Weak transcription	Right Atrium	heart

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