Variant report

Variant	rs6048344
Chromosome Location	chr20:22771364-22771365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1997880	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424462	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424463	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424467	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424471	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2424472	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424474	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424477	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424478	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813469	0.82[AMR][1000 genomes]
rs4815142	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082809	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082843	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6113805	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6132546	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932466	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv912816	chr20:22757960-23062927	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv520547	chr20:22767280-22771404	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6048344	SLC24A3	cis	parietal	SCAN
rs6048344	GINS1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22758000-22772000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:22770400-22775400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:22770600-22772000	Weak transcription	A549	lung
4	chr20:22770600-22775800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:22770800-22772200	Weak transcription	Placenta	Placenta
6	chr20:22771000-22772200	Weak transcription	Fetal Stomach	stomach
7	chr20:22771000-22774200	Weak transcription	Aorta	Aorta
8	chr20:22771000-22774200	Weak transcription	Fetal Muscle Leg	muscle
9	chr20:22771000-22775400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr20:22771000-22776000	Weak transcription	Ovary	ovary

Quick Search:

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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