Variant report

Variant	rs677790
Chromosome Location	chr13:53363783-53363784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs235784	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235785	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs377385	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs402583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs403759	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs403998	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs450836	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs450898	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs459664	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4885981	0.84[ASN][1000 genomes]
rs64262	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9316586	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	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	nsv561655	chr13:53357923-53366885	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
4	nsv561659	chr13:53358598-53367433	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv1054476	chr13:53359853-53380149	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs677790	NEK5	cis	parietal	SCAN
rs677790	KCNRG	cis	parietal	SCAN
rs677790	USP50	trans	parietal	SCAN
rs677790	DLEU2	cis	cerebellum	SCAN
rs677790	ZCCHC2	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53362400-53364200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:53362600-53364800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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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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