Variant report

Variant	rs6014052
Chromosome Location	chr20:53174839-53174840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16999764	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs16999772	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58686390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6014049	0.81[ASN][1000 genomes]
rs6014050	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs6014053	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6014055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014056	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6014058	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023357	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6098064	0.88[TSI][hapmap]
rs6098074	0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62214421	0.89[ASN][1000 genomes]
rs62214425	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7274532	0.88[TSI][hapmap]
rs8117905	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9917433	0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6014052	SALL4	cis	cerebellum	SCAN
rs6014052	RAE1	cis	cerebellum	SCAN
rs6014052	CLEC16A	trans	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53166400-53177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr20:53166800-53176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:53167800-53189200	Weak transcription	Aorta	Aorta
4	chr20:53171200-53187800	Weak transcription	Fetal Muscle Leg	muscle
5	chr20:53171400-53185800	Weak transcription	Fetal Brain Female	brain
6	chr20:53171600-53186800	Weak transcription	Brain Anterior Caudate	brain
7	chr20:53171800-53180200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr20:53172600-53181000	Weak transcription	Brain Germinal Matrix	brain
9	chr20:53174000-53175800	Enhancers	Osteobl	bone
10	chr20:53174200-53175200	Enhancers	NHLF	lung
11	chr20:53174200-53175800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr20:53174200-53181400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr20:53174400-53175200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:53174400-53175200	Flanking Active TSS	HUVEC	blood vessel
15	chr20:53174400-53177600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr20:53174800-53176800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:53174800-53179600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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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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