Variant report

Variant	rs883742
Chromosome Location	chr11:76906468-76906469
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	chr11:76906449..76907116-chr11:77268005..77269240,5	MCF-7	breast:
2	chr11:76906391..76907428-chr11:77080845..77082151,7	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10466708	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11237112	0.92[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12286111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55655554	0.90[EUR][1000 genomes]
rs73495787	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73497617	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73497622	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs867506	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs867716	1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816632	chr11:76751285-76927014	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv897936	chr11:76900813-76935002	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv17589	chr11:76906030-76906635	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs883742	GCNT3	trans	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76880400-76916600	Weak transcription	Right Atrium	heart
2	chr11:76890800-76918400	Weak transcription	Ovary	ovary
3	chr11:76899800-76928200	Strong transcription	Liver	Liver
4	chr11:76903600-76928000	Weak transcription	Colonic Mucosa	Colon
5	chr11:76903600-76928600	Strong transcription	Fetal Intestine Small	intestine
6	chr11:76904000-76908000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:76904000-76909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:76904000-76910600	Weak transcription	HepG2	liver
9	chr11:76904200-76927600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:76904600-76906600	Weak transcription	Gastric	stomach
11	chr11:76904600-76906600	Strong transcription	Pancreas	Pancrea
12	chr11:76904600-76906800	Strong transcription	Spleen	Spleen
13	chr11:76904600-76913200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:76904600-76915600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:76904600-76927800	Strong transcription	Fetal Intestine Large	intestine
16	chr11:76905000-76907000	Strong transcription	Adipose Nuclei	Adipose
17	chr11:76905000-76909600	Weak transcription	Esophagus	oesophagus
18	chr11:76905400-76906800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:76905800-76907000	Enhancers	Fetal Muscle Trunk	muscle
20	chr11:76905800-76908000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr11:76906000-76906600	Genic enhancers	Placenta	Placenta
22	chr11:76906000-76907000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:76906000-76907400	Enhancers	Fetal Muscle Leg	muscle
24	chr11:76906000-76908600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:76906200-76906600	Enhancers	Fetal Stomach	stomach
26	chr11:76906200-76906600	Enhancers	Right Ventricle	heart
27	chr11:76906200-76906800	Enhancers	Psoas Muscle	Psoas
28	chr11:76906200-76907000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr11:76906200-76907000	Enhancers	HSMM	muscle
30	chr11:76906200-76907200	Enhancers	HSMMtube	muscle
31	chr11:76906400-76906800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:76906400-76906800	Enhancers	Fetal Brain Male	brain
33	chr11:76906400-76906800	Enhancers	Left Ventricle	heart
34	chr11:76906400-76907000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:76906400-76907000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr11:76906400-76907000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr11:76906400-76908400	Enhancers	Stomach Mucosa	stomach

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