Variant report

Variant	rs16945988
Chromosome Location	chr16:48265777-48265778
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	chr16:48265466..48265973-chr16:48291256..48291760,2	K562	blood:
2	chr16:48264506..48269686-chr16:48276668..48281172,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102910	Chromatin interaction
ENSG00000121270	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10048092	1.00[ASN][1000 genomes]
rs10221107	1.00[ASN][1000 genomes]
rs10521167	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076561	1.00[ASN][1000 genomes]
rs11076562	1.00[ASN][1000 genomes]
rs11076564	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076565	1.00[ASN][1000 genomes]
rs11552148	1.00[ASN][1000 genomes]
rs11859911	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];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861379	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11863133	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11863233	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11863236	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11863414	0.83[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]
rs11865596	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866312	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.99[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	0.83[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]
rs13331250	1.00[ASN][1000 genomes]
rs13332304	0.83[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]
rs13334052	0.83[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]
rs13334480	0.83[CEU][hapmap]
rs13335504	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]
rs13336542	0.83[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]
rs13336625	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];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336759	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336771	1.00[ASN][1000 genomes]
rs13337955	0.83[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]
rs13338105	0.83[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16945974	0.83[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16945990	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946006	0.83[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946011	0.83[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]
rs16946014	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]
rs16946038	1.00[ASN][1000 genomes]
rs16946039	1.00[ASN][1000 genomes]
rs16946122	0.83[CEU][hapmap];0.83[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	0.83[CEU][hapmap];0.83[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];0.99[EUR][1000 genomes]
rs28378550	1.00[ASN][1000 genomes]
rs28470315	1.00[ASN][1000 genomes]
rs28503414	0.86[AMR][1000 genomes];0.99[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];1.00[EUR][1000 genomes]
rs28617382	1.00[ASN][1000 genomes]
rs28626252	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28654935	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28684834	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28696036	0.86[AMR][1000 genomes];0.99[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28849445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135802	1.00[ASN][1000 genomes]
rs3743989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4325548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528570	1.00[ASN][1000 genomes]
rs5017203	1.00[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59916796	1.00[ASN][1000 genomes]
rs60431412	0.97[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[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187166	0.93[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.91[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];0.97[EUR][1000 genomes]
rs7191181	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7195606	0.83[CEU][hapmap];0.90[YRI][hapmap]
rs7202089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203378	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7203432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203659	1.00[ASN][1000 genomes]
rs73540901	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73542903	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73542904	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73546434	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73546437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73546439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73555628	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562063	1.00[ASN][1000 genomes]
rs7359477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043685	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]
rs8043751	1.00[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][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]
rs8043803	1.00[ASN][1000 genomes]
rs8045819	1.00[ASN][1000 genomes]
rs8046408	1.00[ASN][1000 genomes]
rs8047397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8048098	1.00[ASN][1000 genomes]
rs8049398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051016	1.00[JPT][hapmap]
rs8051186	1.00[ASN][1000 genomes]
rs8051441	1.00[ASN][1000 genomes]
rs8051546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051852	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054117	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054314	1.00[ASN][1000 genomes]
rs8054444	0.85[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.84[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];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8055028	1.00[ASN][1000 genomes]
rs8055128	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8055764	1.00[ASN][1000 genomes]
rs8056100	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];1.00[EUR][1000 genomes]
rs8056143	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8056692	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056846	1.00[ASN][1000 genomes]
rs8058396	0.80[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]
rs8060696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8060722	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8060780	1.00[ASN][1000 genomes]
rs8062407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8190	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9302757	1.00[ASN][1000 genomes]
rs9302758	1.00[ASN][1000 genomes]
rs9923897	1.00[ASN][1000 genomes]
rs9924184	1.00[ASN][1000 genomes]
rs9924497	0.83[ASN][1000 genomes]
rs9925061	1.00[CHB][hapmap]
rs9925591	1.00[ASN][1000 genomes]
rs9925772	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9925935	1.00[ASN][1000 genomes]
rs9926206	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926363	1.00[ASN][1000 genomes]
rs9927756	0.83[CEU][hapmap]
rs9929978	0.83[ASN][1000 genomes]
rs9931294	1.00[ASN][1000 genomes]
rs9932328	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]
rs9932964	1.00[ASN][1000 genomes]
rs9933211	1.00[ASN][1000 genomes]
rs9934833	0.83[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]
rs9935854	0.83[CEU][hapmap]
rs9937882	1.00[ASN][1000 genomes]
rs9938003	1.00[ASN][1000 genomes]
rs9938414	0.83[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]
rs9938490	1.00[ASN][1000 genomes]
rs9938523	1.00[ASN][1000 genomes]
rs9939742	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]
rs9941123	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16945988	LONP2	cis	parietal	SCAN
rs16945988	LONP2	cis	cerebellum	SCAN
rs16945988	GPT2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48263400-48268400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr16:48264200-48265800	Weak transcription	Liver	Liver
3	chr16:48264400-48269200	Weak transcription	Stomach Mucosa	stomach
4	chr16:48264600-48270000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr16:48265200-48266600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:48265200-48267000	Enhancers	HepG2	liver
7	chr16:48265600-48266000	Enhancers	Primary hematopoietic stem cells	blood
8	chr16:48265600-48266000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:48265600-48266000	Weak transcription	A549	lung
10	chr16:48265600-48266400	Enhancers	NHLF	lung
11	chr16:48265600-48266800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:48265600-48266800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr16:48265600-48267000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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