Variant report

Variant	rs235784
Chromosome Location	chr13:53357729-53357730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs235785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377385	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs402583	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs403759	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs403998	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs450836	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450898	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459664	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4885981	0.80[ASN][1000 genomes]
rs64262	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677790	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316586	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv561650	chr13:53357729-53363039	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs235784	USP50	trans	parietal	SCAN
rs235784	KCNRG	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53353800-53361000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr13:53356400-53357800	Enhancers	Fetal Muscle Leg	muscle
3	chr13:53356400-53361000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:53356800-53359400	Weak transcription	Brain Anterior Caudate	brain
5	chr13:53357200-53361200	Weak transcription	Brain Angular Gyrus	brain
6	chr13:53357400-53358800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr13:53357400-53358800	Weak transcription	Brain Substantia Nigra	brain
8	chr13:53357400-53361400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:53357600-53359600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr13:53357600-53361400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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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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