Variant report

Variant	rs1829423
Chromosome Location	chr3:53814197-53814198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11707420	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2278516	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278517	0.90[CEU][hapmap]
rs2278518	0.86[EUR][1000 genomes]
rs2612027	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2680650	0.84[EUR][1000 genomes]
rs3774572	0.85[EUR][1000 genomes]
rs3774579	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs3774585	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3774586	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3774589	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]
rs3774591	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3774602	0.81[JPT][hapmap]
rs3821865	0.87[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4687740	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7617553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9881910	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.97[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	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
rs1829423	MST1R	cis	parietal	SCAN
rs1829423	ACY1	cis	parietal	SCAN
rs1829423	RBM5	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53789800-53814600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:53802400-53818200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:53807400-53819200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:53807600-53814800	Weak transcription	Right Atrium	heart
5	chr3:53807600-53829800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:53808000-53815800	Strong transcription	Fetal Lung	lung
7	chr3:53808200-53814800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:53808200-53817600	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:53808200-53818400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:53808200-53827800	Strong transcription	Fetal Intestine Small	intestine
11	chr3:53808400-53814800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:53808800-53830200	Weak transcription	Pancreas	Pancrea
13	chr3:53809400-53824400	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53811400-53814200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:53811400-53838600	Weak transcription	Spleen	Spleen
16	chr3:53811600-53817600	Weak transcription	Fetal Stomach	stomach
17	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:53811800-53814200	Weak transcription	Lung	lung
19	chr3:53813400-53821400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:53814000-53814200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:53814000-53814400	Enhancers	NHDF-Ad	bronchial
22	chr3:53814000-53814800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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