Variant report

Variant	rs17554301
Chromosome Location	chr11:16402082-16402083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16933090	0.93[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs17470624	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17554911	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4756846	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4757400	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55820833	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030154	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57463944	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72871370	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72871390	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72871402	0.95[EUR][1000 genomes]
rs72873303	0.96[EUR][1000 genomes]
rs72873307	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][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	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17554301	ARNTL	cis	cerebellum	SCAN
rs17554301	PARVA	cis	cerebellum	SCAN
rs17554301	GATAD1	trans	cerebellum	SCAN
rs17554301	PDE3B	cis	cerebellum	SCAN
rs17554301	SPTY2D1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16388200-16414200	Weak transcription	Fetal Intestine Small	intestine
2	chr11:16398200-16403000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:16399400-16404000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:16401800-16403600	Active TSS	K562	blood
5	chr11:16402000-16403000	Enhancers	Pancreatic Islets	Pancreatic Islet

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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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