Variant report

Variant	rs563605
Chromosome Location	chr6:11614620-11614621
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	chr6:11599973..11602605-chr6:11612731..11615608,2	MCF-7	breast:

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs481333	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505571	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571416	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs563605	GCNT2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11607600-11615200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr6:11608200-11615600	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:11610200-11631400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:11610600-11615600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:11611200-11614800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:11611200-11615400	Weak transcription	Lung	lung
7	chr6:11611200-11616400	Weak transcription	Left Ventricle	heart
8	chr6:11611200-11616400	Weak transcription	Ovary	ovary
9	chr6:11611200-11616400	Weak transcription	Psoas Muscle	Psoas
10	chr6:11611200-11622600	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:11612200-11615000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:11612400-11616400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:11612600-11615200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:11612800-11617000	Enhancers	HSMMtube	muscle
15	chr6:11613000-11616600	Enhancers	NHLF	lung
16	chr6:11613000-11616800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:11613200-11615800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:11613200-11616400	Enhancers	NH-A	brain
19	chr6:11613200-11616800	Enhancers	Hela-S3	cervix
20	chr6:11613200-11617000	Enhancers	NHDF-Ad	bronchial
21	chr6:11613200-11617000	Enhancers	Osteobl	bone
22	chr6:11613200-11617200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:11613400-11615000	Enhancers	A549	lung
24	chr6:11613600-11614800	Enhancers	NHEK	skin
25	chr6:11613600-11616200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:11613600-11616800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:11613600-11617000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:11613800-11614800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:11613800-11615600	Enhancers	Adipose Nuclei	Adipose
30	chr6:11613800-11616600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:11613800-11617000	Enhancers	HSMM	muscle
32	chr6:11614000-11615000	Enhancers	HMEC	breast
33	chr6:11614200-11615800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:11614200-11616000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:11614200-11616400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:11614400-11614800	Flanking Active TSS	HUVEC	blood vessel
37	chr6:11614400-11616800	Enhancers	Placenta	Placenta
38	chr6:11614400-11617000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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