Variant report

Variant	rs158542
Chromosome Location	chr20:52639284-52639285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs143706	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs158543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290387	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290418	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs290419	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290455	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290463	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290464	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290465	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290467	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290468	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs384170	0.83[YRI][hapmap]
rs451458	0.87[AMR][1000 genomes]
rs466264	0.83[YRI][hapmap]
rs466416	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs158542	B4GALT5	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52631400-52641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:52633800-52641200	Weak transcription	Brain Angular Gyrus	brain
5	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
6	chr20:52635800-52641800	Enhancers	Brain Substantia Nigra	brain
7	chr20:52636000-52641200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr20:52636600-52640600	Weak transcription	Stomach Mucosa	stomach
9	chr20:52637600-52640400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:52638800-52639400	Weak transcription	Brain Anterior Caudate	brain
11	chr20:52638800-52640000	Weak transcription	Brain Hippocampus Middle	brain
12	chr20:52639200-52640800	Weak transcription	Brain Cingulate Gyrus	brain

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Input of quick search could be:

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

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