Variant report

Variant	rs11676462
Chromosome Location	chr2:54294840-54294841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54184085..54186543-chr2:54292825..54294983,2	K562	blood:
2	chr2:54292163..54295767-chr2:54296379..54301634,7	K562	blood:
3	chr2:54294456..54296366-chr2:54347167..54348766,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10084374	0.84[ASN][1000 genomes]
rs10181999	0.87[ASN][1000 genomes]
rs10496028	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11674724	0.81[ASN][1000 genomes]
rs11890838	0.89[ASN][1000 genomes]
rs11893270	0.83[ASN][1000 genomes]
rs11896815	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898855	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17039547	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17045474	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045488	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2112122	0.83[ASN][1000 genomes]
rs2287643	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2357896	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909459	0.82[AMR][1000 genomes]
rs34498089	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34773403	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671861	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55649409	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55705819	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55930424	0.84[AFR][1000 genomes]
rs56193146	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137964	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62137976	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62137980	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62139336	0.80[AMR][1000 genomes]
rs62140990	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62141002	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545381	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545386	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6711105	0.85[ASN][1000 genomes]
rs6711217	0.82[ASN][1000 genomes]
rs6714450	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721970	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6743455	0.87[ASN][1000 genomes]
rs7559384	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7565453	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7573551	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7576901	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7590819	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11676462	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54278800-54302400	Weak transcription	Left Ventricle	heart
2	chr2:54280800-54310000	Weak transcription	Ovary	ovary
3	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
4	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
6	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
9	chr2:54287400-54295000	Weak transcription	K562	blood
10	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
11	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:54291400-54295200	Weak transcription	Stomach Mucosa	stomach
13	chr2:54291600-54295000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:54291600-54295200	Weak transcription	Psoas Muscle	Psoas
15	chr2:54291600-54298000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:54291800-54295600	Enhancers	HSMMtube	muscle
17	chr2:54291800-54304800	Weak transcription	Fetal Kidney	kidney
18	chr2:54292000-54308400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:54293000-54306000	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:54293200-54295000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:54293200-54295400	Enhancers	Fetal Brain Male	brain
22	chr2:54293200-54306200	Weak transcription	Brain Anterior Caudate	brain
23	chr2:54293200-54306200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:54293400-54295000	Weak transcription	NH-A	brain
25	chr2:54293400-54295000	Weak transcription	Osteobl	bone
26	chr2:54293400-54295800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr2:54293400-54308400	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:54293600-54295000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:54293600-54295000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:54293600-54295200	Weak transcription	NHLF	lung
31	chr2:54293600-54295400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:54293600-54310600	Weak transcription	HSMM	muscle
33	chr2:54293800-54295000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:54293800-54295000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:54293800-54295000	Weak transcription	NHDF-Ad	bronchial
36	chr2:54294000-54295000	Weak transcription	NHEK	skin
37	chr2:54294600-54295200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:54294800-54295600	Enhancers	HMEC	breast
39	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine

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