Variant report

Variant	rs16946014
Chromosome Location	chr16:48272386-48272387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48268351..48270082-chr16:48271401..48273319,2	MCF-7	breast:
2	chr16:48266905..48268593-chr16:48271550..48274010,2	K562	blood:

Variant related genes	Relation type
ENSG00000121270	Chromatin interaction

Extended variants
information (count: 163 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10048092	1.00[ASN][1000 genomes]
rs10221107	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10521167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076561	1.00[ASN][1000 genomes]
rs11076562	1.00[ASN][1000 genomes]
rs11076564	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076565	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11552148	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11859911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860789	1.00[ASN][1000 genomes]
rs11861348	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862480	0.91[CEU][hapmap]
rs11863133	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11863233	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11863236	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11863414	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866312	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12103095	1.00[ASN][1000 genomes]
rs12149230	1.00[ASN][1000 genomes]
rs12149393	1.00[ASN][1000 genomes]
rs13330082	1.00[ASN][1000 genomes]
rs13330105	1.00[ASN][1000 genomes]
rs13331031	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331250	1.00[ASN][1000 genomes]
rs13332304	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13334052	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13334480	1.00[CEU][hapmap]
rs13335504	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13336542	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336771	1.00[ASN][1000 genomes]
rs13337955	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13338105	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13338978	1.00[ASN][1000 genomes]
rs1386053	1.00[ASN][1000 genomes]
rs1545942	1.00[ASN][1000 genomes]
rs16945972	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16945974	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16945988	1.00[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946006	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946011	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946038	1.00[ASN][1000 genomes]
rs16946039	1.00[ASN][1000 genomes]
rs16946122	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843647	1.00[ASN][1000 genomes]
rs2129245	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376623	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28378550	1.00[ASN][1000 genomes]
rs28470315	1.00[ASN][1000 genomes]
rs28503414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28515165	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605399	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28617382	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs28626252	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28654935	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28684834	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28696036	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28716153	1.00[ASN][1000 genomes]
rs28718435	1.00[ASN][1000 genomes]
rs28823370	1.00[ASN][1000 genomes]
rs28842015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28849445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135802	1.00[ASN][1000 genomes]
rs4325548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528570	1.00[ASN][1000 genomes]
rs5017203	0.97[EUR][1000 genomes]
rs56385363	1.00[ASN][1000 genomes]
rs56829365	1.00[ASN][1000 genomes]
rs58409512	1.00[ASN][1000 genomes]
rs58938063	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59916796	1.00[ASN][1000 genomes]
rs60431412	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60745528	1.00[ASN][1000 genomes]
rs60760669	1.00[ASN][1000 genomes]
rs61122640	1.00[ASN][1000 genomes]
rs61676712	1.00[ASN][1000 genomes]
rs6500385	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs70973926	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7184452	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186777	1.00[ASN][1000 genomes]
rs7186982	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187166	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7191181	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7195606	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs7202089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203378	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203659	1.00[ASN][1000 genomes]
rs73540901	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73542903	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73542904	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73546434	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73546437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73546439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73555628	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562063	1.00[ASN][1000 genomes]
rs7359477	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043803	1.00[ASN][1000 genomes]
rs8045819	1.00[ASN][1000 genomes]
rs8046408	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8047397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8048098	1.00[ASN][1000 genomes]
rs8049398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051186	1.00[ASN][1000 genomes]
rs8051441	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8051546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051852	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054117	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054314	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8054444	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8055028	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8055128	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8055764	1.00[ASN][1000 genomes]
rs8056100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8056143	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8056692	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056846	1.00[ASN][1000 genomes]
rs8058396	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8060696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8060722	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8060780	1.00[ASN][1000 genomes]
rs8062407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8190	1.00[ASN][1000 genomes]
rs9302757	1.00[ASN][1000 genomes]
rs9302758	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9923897	1.00[ASN][1000 genomes]
rs9924184	1.00[ASN][1000 genomes]
rs9924497	0.83[ASN][1000 genomes]
rs9925591	1.00[ASN][1000 genomes]
rs9925772	0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs9925935	1.00[ASN][1000 genomes]
rs9926206	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926363	1.00[ASN][1000 genomes]
rs9927756	1.00[CEU][hapmap]
rs9929978	0.83[ASN][1000 genomes]
rs9931294	1.00[ASN][1000 genomes]
rs9932328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9932964	1.00[ASN][1000 genomes]
rs9933211	1.00[ASN][1000 genomes]
rs9934833	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935854	1.00[CEU][hapmap]
rs9937882	1.00[ASN][1000 genomes]
rs9938003	1.00[ASN][1000 genomes]
rs9938414	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938490	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9938523	1.00[ASN][1000 genomes]
rs9939742	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9940038	1.00[CHD][hapmap]
rs9941123	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16946014	LONP2	cis	cerebellum	SCAN
rs16946014	GPT2	cis	parietal	SCAN
rs16946014	LONP2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48269600-48272600	Enhancers	Liver	Liver
2	chr16:48270000-48272400	Enhancers	Fetal Heart	heart
3	chr16:48270200-48277600	Weak transcription	Pancreas	Pancrea
4	chr16:48270400-48272600	Enhancers	HepG2	liver
5	chr16:48272200-48272600	Enhancers	Duodenum Mucosa	Duodenum

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