Variant report

Variant	rs9829714
Chromosome Location	chr3:54209340-54209341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1449335	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2359784	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345101	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352397	0.93[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928003	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4928006	0.93[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs4928007	0.80[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55843545	1.00[ASN][1000 genomes]
rs6445631	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445633	0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs6795550	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72976725	1.00[ASN][1000 genomes]
rs73083991	1.00[ASN][1000 genomes]
rs7649696	0.93[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844833	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9829714	SELK	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54200400-54214800	Weak transcription	Psoas Muscle	Psoas
2	chr3:54206400-54209800	Weak transcription	Hela-S3	cervix
3	chr3:54207800-54212200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:54208400-54212400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:54208600-54213000	Weak transcription	ES-WA7 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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