Variant report

Variant	rs4753501
Chromosome Location	chr11:93512152-93512153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10831102	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12292460	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12803773	0.83[AMR][1000 genomes]
rs1428919	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2434984	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2848477	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4753103	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs585713	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs586293	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs588644	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs598376	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs598427	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs622147	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs625249	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs640864	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs652621	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs655158	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs658181	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs658797	0.91[AFR][1000 genomes]
rs662070	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs675441	0.81[EUR][1000 genomes]
rs675501	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs688634	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs693947	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3322110	chr11:93510554-93512502	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4753501	C11orf54	cis	Esophagus Muscularis	GTEx
rs4753501	C11orf54	cis	Adipose Subcutaneous	GTEx
rs4753501	C11orf54	cis	Heart Left Ventricle	GTEx
rs4753501	C11orf54	cis	Esophagus Mucosa	GTEx
rs4753501	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs4753501	C11orf54	cis	lung	GTEx
rs4753501	C11orf54	cis	Artery Tibial	GTEx
rs4753501	C11orf54	cis	Nerve Tibial	GTEx
rs4753501	C11orf54	cis	Stomach	GTEx
rs4753501	C11orf54	cis	Artery Aorta	GTEx
rs4753501	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs4753501	C11orf54	cis	Muscle Skeletal	GTEx
rs4753501	C11orf54	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93492200-93516600	Weak transcription	Psoas Muscle	Psoas
2	chr11:93492200-93516800	Weak transcription	Right Ventricle	heart
3	chr11:93496000-93513600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:93498000-93516600	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:93498600-93516600	Weak transcription	Hela-S3	cervix
6	chr11:93499200-93516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:93499800-93516600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:93505800-93516600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:93506200-93516600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:93506400-93516600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:93506600-93516600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:93506600-93516600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:93506800-93513000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:93506800-93513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:93506800-93516600	Weak transcription	Brain Germinal Matrix	brain
16	chr11:93507600-93516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:93510400-93516400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:93512000-93516600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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