Variant report

Variant	rs55862533
Chromosome Location	chr3:154748762-154748763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:154747219..154749288-chr3:154751476..154753410,2	K562	blood:
2	chr3:154747251..154749069-chr3:154753697..154755336,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10513467	0.83[AMR][1000 genomes]
rs16824527	0.83[AMR][1000 genomes]
rs16824533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17442246	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1836912	1.00[EUR][1000 genomes]
rs34851137	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860880	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4414805	0.83[AMR][1000 genomes]
rs56317942	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56380855	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56393356	1.00[EUR][1000 genomes]
rs57022891	0.83[AMR][1000 genomes]
rs58120007	0.83[AMR][1000 genomes]
rs60351120	0.83[AMR][1000 genomes]
rs60435073	0.83[AMR][1000 genomes]
rs60948062	0.83[AMR][1000 genomes]
rs73874449	1.00[AMR][1000 genomes]
rs73874454	0.83[AMR][1000 genomes]
rs73874476	0.83[AMR][1000 genomes]
rs73874478	0.83[AMR][1000 genomes]
rs73874489	0.83[AMR][1000 genomes]
rs7643334	0.83[AMR][1000 genomes]
rs9917802	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868930	chr3:154076125-154820242	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1000140	chr3:154336261-154905740	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534289	chr3:154535584-154987166	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv532663	chr3:154561578-154960353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55862533	C18orf54	trans	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154744400-154750200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:154745400-154749400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:154745400-154750400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:154745400-154750400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:154745600-154750400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:154746400-154750400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:154746400-154753400	Weak transcription	K562	blood
8	chr3:154747600-154749000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:154747600-154749400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:154747800-154749000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:154747800-154749200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:154748200-154748800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:154748200-154752800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:154748400-154748800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:154748400-154748800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr3:154748400-154749000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:154748400-154749000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:154748400-154749400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:154748400-154749400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:154748400-154750600	Enhancers	Adipose Nuclei	Adipose
21	chr3:154748400-154751400	Enhancers	Osteobl	bone
22	chr3:154748400-154752600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:154748400-154753800	Enhancers	NHDF-Ad	bronchial
24	chr3:154748600-154749000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:154748600-154749000	Enhancers	HSMMtube	muscle
26	chr3:154748600-154749000	Enhancers	NHLF	lung
27	chr3:154748600-154749200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:154748600-154750800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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