Variant report

Variant	rs9932964
Chromosome Location	chr16:48298315-48298316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10048092	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221107	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10521167	1.00[ASN][1000 genomes]
rs11076561	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076562	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076564	1.00[ASN][1000 genomes]
rs11076565	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552148	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859911	1.00[ASN][1000 genomes]
rs11860789	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861348	1.00[ASN][1000 genomes]
rs11861379	1.00[ASN][1000 genomes]
rs11863414	1.00[ASN][1000 genomes]
rs11865596	1.00[ASN][1000 genomes]
rs11866225	1.00[ASN][1000 genomes]
rs11866529	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12103095	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149230	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149393	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330082	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330105	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331031	1.00[ASN][1000 genomes]
rs13331250	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13332304	1.00[ASN][1000 genomes]
rs13334052	1.00[ASN][1000 genomes]
rs13336264	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13336542	1.00[ASN][1000 genomes]
rs13336625	1.00[ASN][1000 genomes]
rs13336759	1.00[ASN][1000 genomes]
rs13336771	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337955	1.00[ASN][1000 genomes]
rs13338105	1.00[ASN][1000 genomes]
rs13338978	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386053	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545942	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945988	1.00[ASN][1000 genomes]
rs16945990	1.00[ASN][1000 genomes]
rs16946006	1.00[ASN][1000 genomes]
rs16946011	1.00[ASN][1000 genomes]
rs16946014	1.00[ASN][1000 genomes]
rs16946038	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946039	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946122	1.00[ASN][1000 genomes]
rs1843647	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129245	1.00[ASN][1000 genomes]
rs28378550	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470315	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515165	1.00[ASN][1000 genomes]
rs28617382	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716153	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718435	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28823370	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842015	1.00[ASN][1000 genomes]
rs28849445	1.00[ASN][1000 genomes]
rs34135802	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325548	1.00[ASN][1000 genomes]
rs4340327	1.00[ASN][1000 genomes]
rs4528570	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385363	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829365	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58409512	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58938063	1.00[ASN][1000 genomes]
rs59916796	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431412	1.00[ASN][1000 genomes]
rs60745528	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60760669	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61122640	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61676712	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500385	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70973926	1.00[ASN][1000 genomes]
rs7184452	1.00[ASN][1000 genomes]
rs7186777	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186982	1.00[ASN][1000 genomes]
rs7187233	0.82[EUR][1000 genomes]
rs7202089	1.00[ASN][1000 genomes]
rs7203432	1.00[ASN][1000 genomes]
rs7203659	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206909	0.80[EUR][1000 genomes]
rs73555628	1.00[ASN][1000 genomes]
rs73555630	1.00[ASN][1000 genomes]
rs73555643	1.00[ASN][1000 genomes]
rs73562063	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359477	1.00[ASN][1000 genomes]
rs8043685	1.00[ASN][1000 genomes]
rs8043751	1.00[ASN][1000 genomes]
rs8043803	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045819	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046408	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046814	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8047091	0.88[EUR][1000 genomes]
rs8048098	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8049398	1.00[ASN][1000 genomes]
rs8051016	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8051186	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051205	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8051441	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051546	1.00[ASN][1000 genomes]
rs8051852	1.00[ASN][1000 genomes]
rs8054117	1.00[ASN][1000 genomes]
rs8054314	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054444	0.83[ASN][1000 genomes]
rs8055028	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055764	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056692	1.00[ASN][1000 genomes]
rs8056846	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057475	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8058396	1.00[ASN][1000 genomes]
rs8060780	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062407	1.00[ASN][1000 genomes]
rs8190	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302757	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302758	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923897	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9924184	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924497	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925591	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925772	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925935	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926206	1.00[ASN][1000 genomes]
rs9926363	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929978	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9931294	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9932328	1.00[ASN][1000 genomes]
rs9932850	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9933211	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934833	1.00[ASN][1000 genomes]
rs9937882	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9938003	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938414	1.00[ASN][1000 genomes]
rs9938490	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938523	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9932964	LONP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48279400-48312600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:48279600-48311200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:48279600-48320200	Weak transcription	Spleen	Spleen
4	chr16:48280400-48309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr16:48280800-48304000	Weak transcription	Hela-S3	cervix
6	chr16:48281400-48313200	Weak transcription	Right Atrium	heart
7	chr16:48281800-48313200	Weak transcription	Psoas Muscle	Psoas
8	chr16:48285200-48309600	Strong transcription	HepG2	liver
9	chr16:48285800-48298600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:48285800-48306800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr16:48285800-48309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:48286000-48300800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:48286000-48300800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr16:48286000-48300800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr16:48286000-48301200	Strong transcription	Dnd41	blood
16	chr16:48286000-48301400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr16:48286000-48301600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:48286000-48301600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr16:48286000-48313200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr16:48286200-48301200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr16:48286200-48301400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr16:48286200-48301400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr16:48287200-48302000	Strong transcription	Placenta	Placenta
24	chr16:48287400-48320200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr16:48288800-48299600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr16:48289400-48309400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr16:48289400-48313200	Weak transcription	Gastric	stomach
28	chr16:48289400-48320400	Weak transcription	Esophagus	oesophagus
29	chr16:48289800-48306800	Weak transcription	Aorta	Aorta
30	chr16:48290600-48300400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr16:48290600-48313800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr16:48290800-48303800	Weak transcription	Stomach Mucosa	stomach
33	chr16:48290800-48306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr16:48291600-48299800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr16:48291600-48301200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr16:48291600-48305200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:48291600-48309400	Strong transcription	Fetal Intestine Large	intestine
38	chr16:48291800-48300800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr16:48292200-48300600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr16:48292200-48303800	Weak transcription	Fetal Intestine Small	intestine
41	chr16:48292200-48306800	Weak transcription	Right Ventricle	heart
42	chr16:48292200-48313200	Weak transcription	Pancreas	Pancrea
43	chr16:48292400-48299600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr16:48292400-48301800	Strong transcription	HSMM	muscle
45	chr16:48292600-48299400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr16:48293000-48301200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr16:48293400-48299000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr16:48293400-48299200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:48293400-48300800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr16:48293800-48309000	Strong transcription	Liver	Liver

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