Variant report

Variant	rs4625954
Chromosome Location	chr2:55175545-55175546
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr2:55175165-55175694	H1-hESC	embryonic stem cell:	n/a	chr2:55175370-55175377 chr2:55175366-55175378 chr2:55175370-55175377 chr2:55175369-55175378 chr2:55175370-55175377
2	EGR1	chr2:55175335-55175550	K562	blood:	n/a	chr2:55175422-55175435

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10166518	0.84[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs13394146	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4377364	0.82[ASN][1000 genomes]
rs881427	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4625954	PSME4	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55172400-55175600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:55172400-55176000	Enhancers	Fetal Muscle Leg	muscle
5	chr2:55172600-55176400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:55172800-55175800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:55172800-55175800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:55173000-55176600	Weak transcription	K562	blood
9	chr2:55173000-55193400	Weak transcription	Aorta	Aorta
10	chr2:55173200-55179800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:55173200-55187000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:55173200-55203400	Weak transcription	Gastric	stomach
13	chr2:55173400-55184600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:55173600-55176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:55173600-55181200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
18	chr2:55173800-55175600	Enhancers	Adipose Nuclei	Adipose
19	chr2:55173800-55176200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:55173800-55176400	Weak transcription	NHLF	lung
21	chr2:55173800-55178600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:55173800-55178800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:55173800-55180000	Weak transcription	HSMMtube	muscle
24	chr2:55174000-55176200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:55174000-55176400	Weak transcription	NHDF-Ad	bronchial
26	chr2:55174000-55178800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:55174000-55178800	Weak transcription	HSMM	muscle
28	chr2:55174200-55175600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55174400-55176200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:55174400-55176400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55174600-55175800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
33	chr2:55175000-55175600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:55175000-55175600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:55175000-55177800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:55175200-55175600	Enhancers	Brain Cingulate Gyrus	brain
37	chr2:55175200-55175600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:55175200-55175600	Enhancers	Brain Substantia Nigra	brain
39	chr2:55175200-55175800	Enhancers	Brain Anterior Caudate	brain
40	chr2:55175200-55178800	Weak transcription	Osteobl	bone
41	chr2:55175400-55175600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr2:55175400-55175800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:55175400-55176600	Enhancers	Esophagus	oesophagus
44	chr2:55175400-55176600	Enhancers	Fetal Muscle Trunk	muscle
45	chr2:55175400-55193200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links