Variant report

Variant	rs3774589
Chromosome Location	chr3:53817358-53817359
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11707420	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1829423	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2278516	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2278517	0.90[CEU][hapmap]
rs2278518	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2612027	0.87[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs2680650	0.83[EUR][1000 genomes]
rs3774572	0.83[EUR][1000 genomes]
rs3774579	0.86[CEU][hapmap]
rs3774586	0.80[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs3774591	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821865	0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4687740	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7617553	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9881910	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	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
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3774589	ACY1	cis	parietal	SCAN
rs3774589	RBM5	cis	parietal	SCAN
rs3774589	MST1R	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53802400-53818200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:53807400-53819200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:53807600-53829800	Weak transcription	Brain Angular Gyrus	brain
4	chr3:53808200-53817600	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:53808200-53818400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:53808200-53827800	Strong transcription	Fetal Intestine Small	intestine
7	chr3:53808800-53830200	Weak transcription	Pancreas	Pancrea
8	chr3:53809400-53824400	Strong transcription	Fetal Intestine Large	intestine
9	chr3:53811400-53838600	Weak transcription	Spleen	Spleen
10	chr3:53811600-53817600	Weak transcription	Fetal Stomach	stomach
11	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:53813400-53821400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:53815200-53829000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:53815200-53829400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:53815400-53829800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:53816600-53818200	Strong transcription	Lung	lung
17	chr3:53816600-53822800	Strong transcription	Fetal Lung	lung
18	chr3:53816800-53818000	Weak transcription	iPS DF 19.11 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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