Variant report

Variant	rs11712998
Chromosome Location	chr3:53688958-53688959
allele	A/G
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:17)

rs_ID	r²[population]
rs11130376	0.87[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11707976	0.86[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709171	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719110	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721212	1.00[CHB][hapmap]
rs11915489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1460118	0.81[MKK][hapmap]
rs17053283	0.84[YRI][hapmap]
rs17237537	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17309406	1.00[CHB][hapmap]
rs3774524	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6762018	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs6802195	0.82[YRI][hapmap]
rs6804675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819463	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	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	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11712998	IFRD2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53677600-53700000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:53684200-53692200	Weak transcription	Right Atrium	heart
4	chr3:53684800-53698600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:53685400-53690000	Weak transcription	Fetal Brain Male	brain
6	chr3:53685800-53695800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:53687400-53691800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:53688000-53689200	Strong transcription	Fetal Intestine Large	intestine
9	chr3:53688800-53691600	Weak transcription	Fetal Lung	lung

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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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