Variant report

Variant	rs505571
Chromosome Location	chr6:11609092-11609093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs481333	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs528679	0.80[EUR][1000 genomes]
rs563605	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571416	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs605058	0.80[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs505571	GCNT2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11593800-11609800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:11602800-11609200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:11602800-11609800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:11603000-11609200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:11603000-11609400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:11603800-11609200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:11605400-11610400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:11605600-11609600	Flanking Active TSS	HUVEC	blood vessel
9	chr6:11605800-11609200	Enhancers	Brain Angular Gyrus	brain
10	chr6:11606000-11612600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:11606200-11609600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:11606400-11609400	Enhancers	NH-A	brain
13	chr6:11606400-11611200	Enhancers	NHDF-Ad	bronchial
14	chr6:11606600-11611200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:11606800-11609200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:11606800-11609400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:11607000-11609400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:11607600-11609400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:11607600-11609400	Weak transcription	Esophagus	oesophagus
20	chr6:11607600-11609800	Weak transcription	Fetal Heart	heart
21	chr6:11607600-11610000	Weak transcription	Spleen	Spleen
22	chr6:11607600-11615200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:11608000-11609400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:11608000-11609400	Weak transcription	Left Ventricle	heart
25	chr6:11608000-11609400	Enhancers	HSMM	muscle
26	chr6:11608000-11609600	Weak transcription	Brain Anterior Caudate	brain
27	chr6:11608000-11609800	Weak transcription	Right Ventricle	heart
28	chr6:11608000-11610800	Weak transcription	Small Intestine	intestine
29	chr6:11608200-11609400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:11608200-11609400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:11608200-11609400	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:11608200-11609400	Weak transcription	Ovary	ovary
33	chr6:11608200-11609800	Weak transcription	Fetal Lung	lung
34	chr6:11608200-11610000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:11608200-11611000	Weak transcription	Adipose Nuclei	Adipose
36	chr6:11608200-11613600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:11608200-11615600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:11608400-11609400	Weak transcription	Fetal Stomach	stomach
39	chr6:11608400-11609400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:11608400-11610400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:11608800-11609200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:11608800-11610200	Enhancers	Brain Germinal Matrix	brain
43	chr6:11608800-11610600	Enhancers	Osteobl	bone
44	chr6:11608800-11611000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr6:11608800-11611200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:11608800-11611200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:11608800-11611200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:11608800-11611200	Enhancers	NHLF	lung
49	chr6:11608800-11614200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:11609000-11609200	Enhancers	Right Atrium	heart

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