Variant report

Variant	rs16946122
Chromosome Location	chr16:48377901-48377902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:48375297-48379647	K562	blood:	n/a	n/a
2	POLR2A	chr16:48377846-48378584	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48367655..48370253-chr16:48377797..48380677,2	K562	blood:

Variant related genes	Relation type
LONP2	TF binding region
ENSG00000102910	Chromatin interaction
ENSG00000240793	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 4 )

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[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]
rs11076561	1.00[ASN][1000 genomes]
rs11076562	1.00[ASN][1000 genomes]
rs11076564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[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[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]
rs11860789	1.00[ASN][1000 genomes]
rs11861348	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861379	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]
rs11862480	0.91[CEU][hapmap]
rs11863133	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11863233	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11863236	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11863414	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865596	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]
rs11866225	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866312	1.00[CEU][hapmap];0.85[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331250	1.00[ASN][1000 genomes]
rs13332304	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13334052	1.00[CEU][hapmap];0.86[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336625	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]
rs13336759	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]
rs13336771	1.00[ASN][1000 genomes]
rs13337955	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13338105	1.00[CEU][hapmap];0.86[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];0.85[EUR][1000 genomes]
rs16945974	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs16945988	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]
rs16945990	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]
rs16946006	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946011	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946014	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]
rs16946038	1.00[ASN][1000 genomes]
rs16946039	1.00[ASN][1000 genomes]
rs1843647	1.00[ASN][1000 genomes]
rs2129245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376623	0.85[EUR][1000 genomes]
rs28378550	1.00[ASN][1000 genomes]
rs28470315	1.00[ASN][1000 genomes]
rs28503414	0.85[EUR][1000 genomes]
rs28515165	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605399	0.86[EUR][1000 genomes]
rs28617382	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs28626252	0.85[EUR][1000 genomes]
rs28654935	0.85[EUR][1000 genomes]
rs28684834	0.85[EUR][1000 genomes]
rs28696036	0.85[EUR][1000 genomes]
rs28716153	1.00[ASN][1000 genomes]
rs28718435	1.00[ASN][1000 genomes]
rs28823370	1.00[ASN][1000 genomes]
rs28842015	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28849445	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135802	1.00[ASN][1000 genomes]
rs4325548	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340327	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528570	1.00[ASN][1000 genomes]
rs5017203	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56385363	1.00[ASN][1000 genomes]
rs56829365	1.00[ASN][1000 genomes]
rs58409512	1.00[ASN][1000 genomes]
rs58938063	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59916796	1.00[ASN][1000 genomes]
rs60431412	0.93[AMR][1000 genomes];0.86[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	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7184452	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186777	1.00[ASN][1000 genomes]
rs7186982	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187166	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]
rs7191181	0.84[EUR][1000 genomes]
rs7195606	1.00[CEU][hapmap]
rs7202089	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203378	0.86[EUR][1000 genomes]
rs7203432	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203659	1.00[ASN][1000 genomes]
rs73540901	0.85[EUR][1000 genomes]
rs73542903	0.85[EUR][1000 genomes]
rs73542904	0.85[EUR][1000 genomes]
rs73546434	0.86[EUR][1000 genomes]
rs73546437	0.86[EUR][1000 genomes]
rs73546439	0.86[EUR][1000 genomes]
rs73555628	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555630	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73555643	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562063	1.00[ASN][1000 genomes]
rs7359477	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043685	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]
rs8043751	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[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	0.86[EUR][1000 genomes]
rs8048098	1.00[ASN][1000 genomes]
rs8049398	0.83[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	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051852	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054117	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054314	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8054444	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8055028	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8055128	0.83[EUR][1000 genomes]
rs8055764	1.00[ASN][1000 genomes]
rs8056100	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs8056143	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs8056692	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056846	1.00[ASN][1000 genomes]
rs8058396	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8060696	0.86[EUR][1000 genomes]
rs8060722	0.84[EUR][1000 genomes]
rs8060780	1.00[ASN][1000 genomes]
rs8062407	0.86[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	1.00[ASN][1000 genomes]
rs9925935	1.00[ASN][1000 genomes]
rs9926206	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[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[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]
rs9932964	1.00[ASN][1000 genomes]
rs9933211	1.00[ASN][1000 genomes]
rs9934833	1.00[CEU][hapmap];0.86[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];0.86[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:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv833219	chr16:48290595-48459301	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1061708	chr16:48304343-48482594	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv542917	chr16:48304343-48482594	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2758424	chr16:48329437-48479754	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv2758645	chr16:48329437-48479754	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	32 gene(s)	inside rSNPs	diseases
8	esv1837150	chr16:48375777-48470715	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16946122	GPT2	cis	parietal	SCAN
rs16946122	ABCC11	cis	Liver	GTEx
rs16946122	LONP2	cis	parietal	SCAN
rs16946122	LONP2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48338600-48381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr16:48347600-48384800	Weak transcription	Fetal Kidney	kidney
3	chr16:48352200-48395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:48355800-48384800	Weak transcription	Small Intestine	intestine
5	chr16:48363400-48383400	Weak transcription	HUVEC	blood vessel
6	chr16:48364400-48378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr16:48365000-48381400	Weak transcription	Pancreas	Pancrea
8	chr16:48365000-48388200	Weak transcription	Right Atrium	heart
9	chr16:48365200-48378600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr16:48365200-48392400	Strong transcription	Liver	Liver
11	chr16:48367000-48378600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:48367000-48387000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:48367200-48387000	Strong transcription	Primary T cells from cord blood	blood
14	chr16:48367400-48378600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr16:48367400-48387000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:48367600-48378200	Strong transcription	Primary B cells from cord blood	blood
17	chr16:48367600-48378600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr16:48367600-48378800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:48367800-48378600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:48367800-48387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr16:48368200-48378000	Strong transcription	Adipose Nuclei	Adipose
22	chr16:48368200-48378200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr16:48368200-48378600	Strong transcription	HepG2	liver
24	chr16:48368800-48381800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr16:48368800-48384600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr16:48368800-48386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr16:48368800-48387400	Weak transcription	Stomach Mucosa	stomach
28	chr16:48369000-48381400	Weak transcription	Colonic Mucosa	Colon
29	chr16:48369400-48381400	Weak transcription	Brain Germinal Matrix	brain
30	chr16:48369800-48383600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr16:48370000-48381400	Weak transcription	HMEC	breast
32	chr16:48370000-48398600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr16:48370200-48380400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr16:48370400-48381200	Weak transcription	Brain Angular Gyrus	brain
35	chr16:48370400-48389800	Weak transcription	Psoas Muscle	Psoas
36	chr16:48370400-48395000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr16:48370400-48399200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr16:48370600-48399200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:48370800-48395400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr16:48371000-48378800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr16:48371000-48381200	Weak transcription	HSMMtube	muscle
42	chr16:48371000-48384200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr16:48371000-48384200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr16:48371000-48398200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr16:48371200-48378800	Strong transcription	Fetal Stomach	stomach
46	chr16:48371200-48395400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr16:48371400-48378200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr16:48371400-48383400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr16:48371400-48383800	Weak transcription	K562	blood
50	chr16:48371600-48381200	Weak transcription	NHLF	lung

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