Variant report

Variant	rs28823370
Chromosome Location	chr16:48349706-48349707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10048092	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221107	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10521167	1.00[ASN][1000 genomes]
rs11076561	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076562	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076564	1.00[ASN][1000 genomes]
rs11076565	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552148	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859911	1.00[ASN][1000 genomes]
rs11860789	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[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	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149230	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149393	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330082	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330105	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13331031	1.00[ASN][1000 genomes]
rs13331250	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13332304	1.00[ASN][1000 genomes]
rs13334052	1.00[ASN][1000 genomes]
rs13336264	0.81[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	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337955	1.00[ASN][1000 genomes]
rs13338105	1.00[ASN][1000 genomes]
rs13338978	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386053	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545942	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[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	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946122	1.00[ASN][1000 genomes]
rs1843647	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129245	1.00[ASN][1000 genomes]
rs28378550	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470315	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515165	1.00[ASN][1000 genomes]
rs28617382	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716153	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718435	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842015	1.00[ASN][1000 genomes]
rs28849445	1.00[ASN][1000 genomes]
rs34135802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325548	1.00[ASN][1000 genomes]
rs4340327	1.00[ASN][1000 genomes]
rs4528570	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385363	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829365	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58409512	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58938063	1.00[ASN][1000 genomes]
rs59916796	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60431412	1.00[ASN][1000 genomes]
rs60745528	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60760669	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61122640	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61676712	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500385	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70973926	1.00[ASN][1000 genomes]
rs7184452	1.00[ASN][1000 genomes]
rs7186777	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[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	0.91[AMR][1000 genomes];0.85[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	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[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	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045819	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046408	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046814	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8047091	0.88[EUR][1000 genomes]
rs8048098	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8049398	1.00[ASN][1000 genomes]
rs8051016	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8051186	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051205	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8051441	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[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	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054444	0.83[ASN][1000 genomes]
rs8055028	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055764	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056692	1.00[ASN][1000 genomes]
rs8056846	0.93[AMR][1000 genomes];0.93[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062407	1.00[ASN][1000 genomes]
rs8190	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302757	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302758	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923897	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924184	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924497	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925591	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925772	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925935	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926206	1.00[ASN][1000 genomes]
rs9926363	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929978	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9931294	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9932328	1.00[ASN][1000 genomes]
rs9932850	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9932964	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933211	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934833	1.00[ASN][1000 genomes]
rs9937882	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938003	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938414	1.00[ASN][1000 genomes]
rs9938490	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9938523	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28823370	LONP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48325000-48350800	Weak transcription	NHLF	lung
2	chr16:48330400-48354600	Weak transcription	Stomach Mucosa	stomach
3	chr16:48334600-48350800	Weak transcription	NH-A	brain
4	chr16:48334800-48361400	Strong transcription	Liver	Liver
5	chr16:48338000-48351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:48338400-48350800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:48338600-48352600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:48338600-48352600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr16:48338600-48381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr16:48339400-48368000	Weak transcription	Colonic Mucosa	Colon
11	chr16:48341400-48350600	Weak transcription	Osteobl	bone
12	chr16:48342200-48368000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr16:48343400-48375600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:48344600-48368200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr16:48345000-48351600	Weak transcription	Small Intestine	intestine
16	chr16:48345200-48350600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr16:48345200-48350800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr16:48345200-48350800	Weak transcription	HUVEC	blood vessel
19	chr16:48345200-48351000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr16:48345200-48351000	Weak transcription	HMEC	breast
21	chr16:48345200-48351200	Weak transcription	HSMM	muscle
22	chr16:48345600-48351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:48345800-48351000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr16:48345800-48351400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:48345800-48351600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr16:48345800-48352600	Weak transcription	Fetal Heart	heart
27	chr16:48345800-48363200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr16:48346000-48352400	Weak transcription	Brain Angular Gyrus	brain
29	chr16:48346000-48355000	Weak transcription	Psoas Muscle	Psoas
30	chr16:48346600-48350800	Weak transcription	Primary T cells from cord blood	blood
31	chr16:48346600-48351400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr16:48346600-48364200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr16:48346600-48368200	Weak transcription	Colon Smooth Muscle	Colon
34	chr16:48346800-48350800	Weak transcription	HSMMtube	muscle
35	chr16:48346800-48350800	Weak transcription	NHEK	skin
36	chr16:48346800-48351600	Weak transcription	Spleen	Spleen
37	chr16:48346800-48352400	Weak transcription	Fetal Brain Male	brain
38	chr16:48346800-48368200	Weak transcription	A549	lung
39	chr16:48347000-48350000	Weak transcription	Fetal Stomach	stomach
40	chr16:48347000-48350800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr16:48347000-48351000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr16:48347000-48351000	Weak transcription	Thymus	Thymus
43	chr16:48347000-48351600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr16:48347000-48351600	Weak transcription	Right Ventricle	heart
45	chr16:48347000-48351800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:48347000-48352000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr16:48347000-48352200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:48347000-48352200	Weak transcription	Lung	lung
49	chr16:48347000-48352400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr16:48347000-48353000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links