Variant report

Variant	rs10520268
Chromosome Location	chr4:174988271-174988272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10027364	0.84[EUR][1000 genomes]
rs10520269	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13108199	0.85[EUR][1000 genomes]
rs13128967	0.82[EUR][1000 genomes]
rs2164378	0.81[EUR][1000 genomes]
rs2196372	0.84[EUR][1000 genomes]
rs2332800	0.92[EUR][1000 genomes]
rs28831457	0.99[EUR][1000 genomes]
rs28839916	0.87[EUR][1000 genomes]
rs4695906	0.95[EUR][1000 genomes]
rs7670262	0.81[AFR][1000 genomes]
rs9996330	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9998435	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9999168	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830155	chr4:174943809-175136483	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv508335	chr4:174961722-174995092	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10520268	GALNTL6	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174984800-174988800	Weak transcription	Fetal Lung	lung
2	chr4:174987800-174988600	Enhancers	Colon Smooth Muscle	Colon
3	chr4:174988000-174988800	Bivalent Enhancer	Fetal Brain Male	brain
4	chr4:174988200-174988400	Enhancers	Stomach Smooth Muscle	stomach
5	chr4:174988200-174988600	Enhancers	Left Ventricle	heart
6	chr4:174988200-174989800	Enhancers	Aorta	Aorta

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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