Variant report

Variant	rs643261
Chromosome Location	chr11:93507066-93507067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93473228..93477931-chr11:93504576..93509493,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166012	Chromatin interaction
ENSG00000182919	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10831103	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11020511	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11020515	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11603339	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11603364	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2895508	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596052	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs607349	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs613610	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs621801	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635963	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644306	1.00[CHB][hapmap]
rs668546	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs677867	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685865	0.91[EUR][1000 genomes]
rs7310	1.00[CHB][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs643261	C11orf54	cis	Esophagus Muscularis	GTEx
rs643261	C11orf54	cis	Artery Aorta	GTEx
rs643261	C11orf54	cis	Esophagus Mucosa	GTEx
rs643261	C11orf54	cis	Artery Tibial	GTEx
rs643261	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93478800-93508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:93492200-93507400	Weak transcription	Aorta	Aorta
3	chr11:93492200-93516600	Weak transcription	Psoas Muscle	Psoas
4	chr11:93492200-93516800	Weak transcription	Right Ventricle	heart
5	chr11:93493800-93507200	Weak transcription	Ovary	ovary
6	chr11:93496000-93513600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:93498000-93516600	Weak transcription	Brain Hippocampus Middle	brain
8	chr11:93498600-93516600	Weak transcription	Hela-S3	cervix
9	chr11:93499200-93516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:93499800-93516600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:93505000-93507400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:93505800-93516600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:93506200-93516600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:93506400-93516600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:93506600-93510000	Weak transcription	Spleen	Spleen
16	chr11:93506600-93516600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:93506600-93516600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:93506800-93507200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:93506800-93507200	Enhancers	HepG2	liver
20	chr11:93506800-93513000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:93506800-93513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:93506800-93516600	Weak transcription	Brain Germinal Matrix	brain
23	chr11:93507000-93507400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:93507000-93507600	Enhancers	Lung	lung

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