Variant report

Variant	rs12280776
Chromosome Location	chr11:62250237-62250238
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	chr11:62249543..62252001-chr11:62311288..62312995,2	MCF-7	breast:
2	chr11:62243588..62245637-chr11:62248831..62251518,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11231105	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11231140	1.00[AMR][1000 genomes]
rs12279778	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12283164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12287248	1.00[AMR][1000 genomes]
rs17157361	1.00[AMR][1000 genomes]
rs34709729	1.00[AMR][1000 genomes]
rs55774907	1.00[AMR][1000 genomes]
rs57293370	1.00[AMR][1000 genomes]
rs57575327	1.00[AMR][1000 genomes]
rs58479396	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59314885	1.00[AMR][1000 genomes]
rs60928821	1.00[AMR][1000 genomes]
rs61524789	1.00[AMR][1000 genomes]
rs7118805	1.00[AMR][1000 genomes]
rs7126915	1.00[AMR][1000 genomes]
rs73498073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73502133	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv1038606	chr11:62105613-62251969	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
4	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
5	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
6	nsv345	chr11:62225251-62270254	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv897621	chr11:62230309-62290170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12280776	C11orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62231200-62264600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:62240400-62254400	Weak transcription	Right Ventricle	heart
3	chr11:62245000-62250400	Enhancers	Placenta	Placenta
4	chr11:62246200-62252000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:62247800-62255200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:62247800-62257000	Weak transcription	NHLF	lung
7	chr11:62247800-62264600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:62247800-62266600	Weak transcription	Esophagus	oesophagus
9	chr11:62247800-62272600	Weak transcription	Aorta	Aorta
10	chr11:62248000-62250600	Enhancers	HepG2	liver
11	chr11:62248400-62250800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:62248600-62255000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:62248600-62255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:62248600-62255200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:62248600-62255600	Weak transcription	Osteobl	bone
16	chr11:62248600-62256800	Weak transcription	NH-A	brain
17	chr11:62248600-62264600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:62248800-62254400	Weak transcription	Fetal Intestine Small	intestine
19	chr11:62248800-62254400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:62248800-62255200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:62248800-62258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:62249000-62251800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:62249000-62254200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:62249000-62255600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:62249000-62256800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:62249000-62256800	Weak transcription	A549	lung
27	chr11:62249000-62264600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:62249200-62254600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:62249600-62251800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:62250000-62250800	Enhancers	Placenta Amnion	Placenta Amnion

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