Variant report

Variant	rs55649409
Chromosome Location	chr2:54291644-54291645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10084374	0.83[ASN][1000 genomes]
rs10181999	0.85[ASN][1000 genomes]
rs10496028	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11674724	0.81[ASN][1000 genomes]
rs11676462	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11890838	0.92[ASN][1000 genomes]
rs11893270	0.86[ASN][1000 genomes]
rs11896815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11898855	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17039547	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045474	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045488	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112122	0.81[ASN][1000 genomes]
rs2287643	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2357896	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909459	0.83[AMR][1000 genomes]
rs34498089	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34773403	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671746	0.80[AMR][1000 genomes]
rs4671861	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55692047	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55705819	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55930424	0.83[AFR][1000 genomes]
rs56193146	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56302494	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62137964	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62137976	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62137980	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62139336	0.82[AMR][1000 genomes]
rs62140990	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62141002	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545381	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6545386	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6711105	0.84[ASN][1000 genomes]
rs6711217	0.81[ASN][1000 genomes]
rs6714450	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6721970	0.88[AMR][1000 genomes]
rs6743455	0.85[ASN][1000 genomes]
rs6748976	0.82[ASN][1000 genomes]
rs72799298	0.82[ASN][1000 genomes]
rs7559384	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7565453	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573551	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7576901	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7590819	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9631059	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55649409	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
2	chr2:54278800-54302400	Weak transcription	Left Ventricle	heart
3	chr2:54280000-54292400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:54280800-54310000	Weak transcription	Ovary	ovary
5	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
6	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
8	chr2:54281200-54292400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:54282200-54293800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:54283400-54292400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:54287200-54291800	Weak transcription	HSMMtube	muscle
14	chr2:54287200-54293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
16	chr2:54287400-54295000	Weak transcription	K562	blood
17	chr2:54287600-54292600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:54287800-54292400	Weak transcription	NH-A	brain
19	chr2:54288000-54291800	Weak transcription	Osteobl	bone
20	chr2:54288000-54292200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:54288000-54292200	Weak transcription	NHDF-Ad	bronchial
22	chr2:54288600-54292200	Enhancers	Fetal Brain Male	brain
23	chr2:54288800-54292200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
25	chr2:54290000-54293000	Enhancers	Brain Substantia Nigra	brain
26	chr2:54290200-54292600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:54290600-54291800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:54290600-54293200	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:54290600-54293600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:54290600-54293800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:54290600-54294400	Enhancers	HMEC	breast
32	chr2:54290800-54292000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:54290800-54292800	Enhancers	NHEK	skin
34	chr2:54291000-54293800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:54291200-54291800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:54291200-54292200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:54291200-54293000	Enhancers	Brain Hippocampus Middle	brain
38	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:54291400-54292000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:54291400-54295200	Weak transcription	Stomach Mucosa	stomach
41	chr2:54291600-54292000	Weak transcription	HSMM	muscle
42	chr2:54291600-54292600	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:54291600-54293600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:54291600-54295000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:54291600-54295200	Weak transcription	Psoas Muscle	Psoas
46	chr2:54291600-54298000	Weak transcription	Primary B cells from peripheral blood	blood

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