Variant report

Variant	rs12528566
Chromosome Location	chr6:109738148-109738149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11753645	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11757877	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12524502	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12528712	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13192476	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13195517	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199519	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13203252	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1322818	0.80[AMR][1000 genomes]
rs2275652	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34131679	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34292461	0.80[AMR][1000 genomes]
rs34320275	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34533653	0.80[AMR][1000 genomes]
rs35452836	0.81[EUR][1000 genomes]
rs35969918	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3757238	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799835	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799840	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4428538	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61076041	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61233650	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61318425	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67857472	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6929208	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3411767	chr6:109738124-109738562	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12528566	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12528566	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12528566	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12528566	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12528566	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
2	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
4	chr6:109724400-109750400	Weak transcription	Ovary	ovary
5	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
6	chr6:109731400-109745200	Weak transcription	Pancreas	Pancrea
7	chr6:109735200-109750200	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:109735600-109750000	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:109735800-109742000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:109736400-109740400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:109736600-109760800	Weak transcription	Brain Angular Gyrus	brain
12	chr6:109737000-109745400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:109737000-109745400	Weak transcription	Left Ventricle	heart
14	chr6:109737400-109750200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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