Variant report

Variant	rs12149230
Chromosome Location	chr16:48316188-48316189
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:48311363..48313825-chr16:48314630..48317247,2	K562	blood:
2	chr16:48310047..48313825-chr16:48313947..48317247,4	K562	blood:

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10048092	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221107	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10521167	1.00[ASN][1000 genomes]
rs11076561	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076562	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076564	1.00[ASN][1000 genomes]
rs11076565	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552148	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859911	1.00[ASN][1000 genomes]
rs11860789	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12103095	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149393	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330082	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330105	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331031	1.00[ASN][1000 genomes]
rs13331250	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13332304	1.00[ASN][1000 genomes]
rs13334052	1.00[ASN][1000 genomes]
rs13336264	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13336542	1.00[ASN][1000 genomes]
rs13336625	1.00[ASN][1000 genomes]
rs13336759	1.00[ASN][1000 genomes]
rs13336771	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337955	1.00[ASN][1000 genomes]
rs13338105	1.00[ASN][1000 genomes]
rs13338978	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386053	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545942	0.95[AMR][1000 genomes];0.91[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	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946039	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946122	1.00[ASN][1000 genomes]
rs1843647	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129245	1.00[ASN][1000 genomes]
rs28378550	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470315	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515165	1.00[ASN][1000 genomes]
rs28617382	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716153	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718435	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28823370	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842015	1.00[ASN][1000 genomes]
rs28849445	1.00[ASN][1000 genomes]
rs34135802	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325548	1.00[ASN][1000 genomes]
rs4340327	1.00[ASN][1000 genomes]
rs4528570	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385363	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829365	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58409512	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58938063	1.00[ASN][1000 genomes]
rs59916796	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431412	1.00[ASN][1000 genomes]
rs60745528	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60760669	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61122640	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61676712	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500385	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70973926	1.00[ASN][1000 genomes]
rs7184452	1.00[ASN][1000 genomes]
rs7186777	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186982	1.00[ASN][1000 genomes]
rs7187233	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7202089	1.00[ASN][1000 genomes]
rs7203432	1.00[ASN][1000 genomes]
rs7203659	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206909	0.82[EUR][1000 genomes]
rs73555628	1.00[ASN][1000 genomes]
rs73555630	1.00[ASN][1000 genomes]
rs73555643	1.00[ASN][1000 genomes]
rs73562063	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045819	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046408	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046814	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8047091	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8048098	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8049398	1.00[ASN][1000 genomes]
rs8050120	0.81[EUR][1000 genomes]
rs8051016	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8051186	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051205	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8051441	0.90[AMR][1000 genomes];0.96[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	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054444	0.83[ASN][1000 genomes]
rs8055028	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055764	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056692	1.00[ASN][1000 genomes]
rs8056846	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057475	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8058396	1.00[ASN][1000 genomes]
rs8060780	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062407	1.00[ASN][1000 genomes]
rs8190	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302757	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923897	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924184	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924497	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925591	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925772	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925935	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926206	1.00[ASN][1000 genomes]
rs9926363	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929978	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9931294	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9932328	1.00[ASN][1000 genomes]
rs9932850	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9932964	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933211	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934833	1.00[ASN][1000 genomes]
rs9937882	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938003	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938414	1.00[ASN][1000 genomes]
rs9938490	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938523	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12149230	LONP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48279600-48320200	Weak transcription	Spleen	Spleen
2	chr16:48287400-48320200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:48289400-48320400	Weak transcription	Esophagus	oesophagus
4	chr16:48293800-48320400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:48294800-48320400	Weak transcription	Lung	lung
6	chr16:48297200-48323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr16:48297600-48318600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr16:48297600-48319800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr16:48297600-48321000	Weak transcription	Fetal Brain Male	brain
10	chr16:48297800-48319800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:48297800-48320800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:48297800-48320800	Weak transcription	Brain Germinal Matrix	brain
13	chr16:48297800-48320800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:48297800-48320800	Weak transcription	Small Intestine	intestine
15	chr16:48299000-48320400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr16:48300200-48320200	Weak transcription	Fetal Stomach	stomach
17	chr16:48302800-48321000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr16:48304400-48317000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:48304800-48318400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr16:48304800-48319200	Weak transcription	Hela-S3	cervix
21	chr16:48305200-48328600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr16:48305400-48320400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr16:48305600-48317000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr16:48306000-48317000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr16:48307200-48319000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr16:48307200-48320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:48307200-48321000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr16:48310200-48316200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:48310400-48317600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr16:48310400-48320200	Weak transcription	Aorta	Aorta
31	chr16:48310600-48316600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr16:48310600-48319000	Weak transcription	Fetal Brain Female	brain
33	chr16:48310800-48317200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:48311000-48317000	Weak transcription	Colon Smooth Muscle	Colon
35	chr16:48311200-48318200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr16:48311400-48319800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr16:48311400-48320200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr16:48311600-48317200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr16:48311800-48320200	Weak transcription	Colonic Mucosa	Colon
40	chr16:48311800-48320200	Weak transcription	NHLF	lung
41	chr16:48311800-48320400	Weak transcription	NHDF-Ad	bronchial
42	chr16:48311800-48320800	Weak transcription	HSMMtube	muscle
43	chr16:48312000-48318600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr16:48312400-48316600	Weak transcription	Primary T cells from cord blood	blood
45	chr16:48312400-48317000	Enhancers	Fetal Heart	heart
46	chr16:48312400-48318400	Weak transcription	Placenta	Placenta
47	chr16:48312400-48319000	Weak transcription	Fetal Intestine Small	intestine
48	chr16:48312400-48319400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr16:48312600-48316800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr16:48312800-48319000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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