Variant report

Variant	rs2962540
Chromosome Location	chr5:145450586-145450587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:145446984..145448552-chr5:145450053..145451933,2	K562	blood:

Extended variants
information (count: 172 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs10491260	0.83[AFR][1000 genomes]
rs10491261	0.83[AFR][1000 genomes]
rs10515564	0.83[AFR][1000 genomes]
rs11167927	0.84[ASW][hapmap]
rs11167932	0.83[AFR][1000 genomes]
rs11167933	0.83[AFR][1000 genomes]
rs11167934	0.83[AFR][1000 genomes]
rs11540214	0.83[AFR][1000 genomes]
rs11540215	0.83[AFR][1000 genomes]
rs11540217	0.83[AFR][1000 genomes]
rs11748238	0.84[ASW][hapmap]
rs11948016	0.83[AFR][1000 genomes]
rs11948180	0.83[AFR][1000 genomes]
rs11948314	0.83[AFR][1000 genomes]
rs11949351	0.83[AFR][1000 genomes]
rs11949352	0.83[AFR][1000 genomes]
rs11949703	0.83[AFR][1000 genomes]
rs11951553	0.83[AFR][1000 genomes]
rs11952697	0.83[AFR][1000 genomes]
rs11953517	0.83[AFR][1000 genomes]
rs11954083	0.83[AFR][1000 genomes]
rs11954750	0.83[AFR][1000 genomes]
rs11954870	0.83[AFR][1000 genomes]
rs11954923	0.83[AFR][1000 genomes]
rs11954977	0.83[AFR][1000 genomes]
rs11957830	0.83[AFR][1000 genomes]
rs11957888	0.83[AFR][1000 genomes]
rs11957998	0.83[AFR][1000 genomes]
rs11959805	0.83[AFR][1000 genomes]
rs11960510	0.83[AFR][1000 genomes]
rs12153109	0.83[AFR][1000 genomes]
rs12153238	0.83[AFR][1000 genomes]
rs12186642	0.83[AFR][1000 genomes]
rs12187128	0.83[AFR][1000 genomes]
rs12187649	0.83[AFR][1000 genomes]
rs12187913	0.83[AFR][1000 genomes]
rs12188581	0.83[AFR][1000 genomes]
rs12188772	0.83[AFR][1000 genomes]
rs13153675	0.83[AFR][1000 genomes]
rs13154735	0.83[AFR][1000 genomes]
rs13157279	0.83[AFR][1000 genomes]
rs13159380	0.83[AFR][1000 genomes]
rs13161036	0.83[AFR][1000 genomes]
rs13161075	0.83[AFR][1000 genomes]
rs13161659	0.83[AFR][1000 genomes]
rs13163457	0.84[ASW][hapmap];1.00[MKK][hapmap]
rs13164882	0.83[AFR][1000 genomes]
rs13171828	0.83[AFR][1000 genomes]
rs13174055	0.83[AFR][1000 genomes]
rs13175806	0.83[AFR][1000 genomes]
rs13176784	0.83[AFR][1000 genomes]
rs13178370	0.83[AFR][1000 genomes]
rs13178516	0.83[AFR][1000 genomes]
rs13178840	0.83[AFR][1000 genomes]
rs13180113	0.83[AFR][1000 genomes]
rs13181074	0.83[AFR][1000 genomes]
rs13182302	0.83[AFR][1000 genomes]
rs13182567	0.83[AFR][1000 genomes]
rs13182838	0.83[AFR][1000 genomes]
rs13184702	0.83[AFR][1000 genomes]
rs13185586	0.83[AFR][1000 genomes]
rs13185805	0.83[AFR][1000 genomes]
rs13186694	0.83[AFR][1000 genomes]
rs13186701	0.83[AFR][1000 genomes]
rs1395277	0.83[AFR][1000 genomes]
rs1506431	0.83[AFR][1000 genomes]
rs17212373	0.83[AFR][1000 genomes]
rs17428100	0.83[AFR][1000 genomes]
rs17428465	0.83[AFR][1000 genomes]
rs17428570	0.83[AFR][1000 genomes]
rs17428724	0.83[AFR][1000 genomes]
rs17492851	0.83[AFR][1000 genomes]
rs17492893	0.83[AFR][1000 genomes]
rs17493090	0.83[AFR][1000 genomes]
rs17493851	0.83[AFR][1000 genomes]
rs17500456	0.83[AFR][1000 genomes]
rs17500504	0.83[AFR][1000 genomes]
rs17500927	0.83[AFR][1000 genomes]
rs17796870	0.83[AFR][1000 genomes]
rs187465	0.84[ASW][hapmap];1.00[MKK][hapmap]
rs1985600	0.83[AFR][1000 genomes]
rs2015248	0.83[AFR][1000 genomes]
rs2024055	0.83[AFR][1000 genomes]
rs2024057	0.83[AFR][1000 genomes]
rs2292172	0.83[AFR][1000 genomes]
rs2292173	0.83[AFR][1000 genomes]
rs2302036	0.83[AFR][1000 genomes]
rs248779	0.84[ASW][hapmap];1.00[MKK][hapmap]
rs2895647	0.83[AFR][1000 genomes]
rs2895648	0.83[AFR][1000 genomes]
rs2895649	0.83[AFR][1000 genomes]
rs2895650	0.83[AFR][1000 genomes]
rs2962541	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33914983	0.83[AFR][1000 genomes]
rs34014355	0.83[AFR][1000 genomes]
rs34049009	0.83[AFR][1000 genomes]
rs34071526	0.83[AFR][1000 genomes]
rs34078408	0.83[AFR][1000 genomes]
rs34160255	0.83[AFR][1000 genomes]
rs34170515	0.83[AFR][1000 genomes]
rs34272709	0.83[AFR][1000 genomes]
rs34342344	0.83[AFR][1000 genomes]
rs34345997	0.83[AFR][1000 genomes]
rs34404385	0.83[AFR][1000 genomes]
rs34482773	0.83[AFR][1000 genomes]
rs34516108	0.83[AFR][1000 genomes]
rs34529192	0.83[AFR][1000 genomes]
rs34533649	0.83[AFR][1000 genomes]
rs34581962	0.83[AFR][1000 genomes]
rs34601905	0.83[AFR][1000 genomes]
rs34683303	0.83[AFR][1000 genomes]
rs34774165	0.83[AFR][1000 genomes]
rs34818690	0.83[AFR][1000 genomes]
rs35048686	0.83[AFR][1000 genomes]
rs35150639	0.83[AFR][1000 genomes]
rs35228139	0.83[AFR][1000 genomes]
rs35238125	0.83[AFR][1000 genomes]
rs35262581	0.83[AFR][1000 genomes]
rs35421875	0.83[AFR][1000 genomes]
rs35424128	0.83[AFR][1000 genomes]
rs35436549	0.83[AFR][1000 genomes]
rs35652702	0.83[AFR][1000 genomes]
rs35658996	0.83[AFR][1000 genomes]
rs35749752	0.83[AFR][1000 genomes]
rs35801832	0.83[AFR][1000 genomes]
rs35821418	0.83[AFR][1000 genomes]
rs35825928	0.83[AFR][1000 genomes]
rs35868039	0.83[AFR][1000 genomes]
rs35869904	0.83[AFR][1000 genomes]
rs36059140	0.83[AFR][1000 genomes]
rs36095232	0.83[AFR][1000 genomes]
rs36102990	0.83[AFR][1000 genomes]
rs3749994	0.83[AFR][1000 genomes]
rs3763373	0.83[AFR][1000 genomes]
rs3797628	0.83[AFR][1000 genomes]
rs3822623	0.83[AFR][1000 genomes]
rs3828935	0.83[AFR][1000 genomes]
rs41338847	0.83[AFR][1000 genomes]
rs4413574	0.83[AFR][1000 genomes]
rs4443471	0.83[AFR][1000 genomes]
rs4705119	0.83[AFR][1000 genomes]
rs4705398	0.83[AFR][1000 genomes]
rs4705438	0.83[AFR][1000 genomes]
rs4913062	0.83[AFR][1000 genomes]
rs4913063	0.83[AFR][1000 genomes]
rs4913064	0.83[AFR][1000 genomes]
rs4913067	0.83[AFR][1000 genomes]
rs55665974	0.83[AFR][1000 genomes]
rs55681213	0.83[AFR][1000 genomes]
rs55782203	0.83[AFR][1000 genomes]
rs55812375	0.83[AFR][1000 genomes]
rs56278005	0.83[AFR][1000 genomes]
rs56338615	0.83[AFR][1000 genomes]
rs56393319	0.83[AFR][1000 genomes]
rs56410805	0.83[AFR][1000 genomes]
rs62373771	0.83[AFR][1000 genomes]
rs62373785	0.83[AFR][1000 genomes]
rs62373786	0.83[AFR][1000 genomes]
rs62373789	0.83[AFR][1000 genomes]
rs62373798	0.83[AFR][1000 genomes]
rs62373801	0.83[AFR][1000 genomes]
rs62373819	0.83[AFR][1000 genomes]
rs62373824	0.83[AFR][1000 genomes]
rs66538287	0.83[AFR][1000 genomes]
rs67051761	0.83[AFR][1000 genomes]
rs67598659	0.83[AFR][1000 genomes]
rs67829086	0.83[AFR][1000 genomes]
rs67986716	0.83[AFR][1000 genomes]
rs71594528	0.83[AFR][1000 genomes]
rs72822286	0.83[AFR][1000 genomes]
rs7443214	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2962540	GLRX	trans	parietal	SCAN
rs2962540	LARS	cis	cerebellum	SCAN
rs2962540	LARS	cis	Thyroid	GTEx
rs2962540	LARS	cis	parietal	SCAN
rs2962540	LARS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145412600-145453200	Weak transcription	Pancreas	Pancrea
2	chr5:145429600-145459600	Weak transcription	Stomach Mucosa	stomach
3	chr5:145434400-145450800	Weak transcription	Brain Anterior Caudate	brain
4	chr5:145436000-145451200	Weak transcription	HepG2	liver
5	chr5:145442400-145461200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:145442800-145450800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:145443200-145458000	Weak transcription	Liver	Liver
8	chr5:145443600-145461000	Weak transcription	Colonic Mucosa	Colon
9	chr5:145444000-145451000	Weak transcription	Fetal Stomach	stomach
10	chr5:145447400-145455000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:145447600-145455400	Weak transcription	Fetal Intestine Large	intestine
12	chr5:145447800-145450600	Weak transcription	Esophagus	oesophagus
13	chr5:145447800-145452800	Weak transcription	Gastric	stomach
14	chr5:145447800-145453200	Weak transcription	Right Ventricle	heart
15	chr5:145448000-145460000	Weak transcription	Fetal Intestine Small	intestine
16	chr5:145448200-145455600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:145448400-145450600	Weak transcription	NHEK	skin
18	chr5:145448400-145458000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:145448600-145455800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:145448800-145450800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:145449800-145451800	Enhancers	GM12878-XiMat	blood
22	chr5:145449800-145454200	Enhancers	Left Ventricle	heart
23	chr5:145450000-145451600	Weak transcription	Small Intestine	intestine
24	chr5:145450000-145458600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:145450200-145450600	Enhancers	Right Atrium	heart
26	chr5:145450200-145451000	Enhancers	Psoas Muscle	Psoas
27	chr5:145450200-145451600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:145450400-145450600	Enhancers	Fetal Heart	heart
29	chr5:145450400-145451600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:145450400-145451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:145450400-145451800	Enhancers	Aorta	Aorta
32	chr5:145450400-145451800	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links