Variant report

Variant	rs3821865
Chromosome Location	chr3:53802295-53802296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11707420	0.87[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs12487452	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1829423	0.87[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2278516	0.91[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278517	0.95[CEU][hapmap]
rs2278518	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2612027	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2680650	0.85[EUR][1000 genomes]
rs3774568	0.81[ASN][1000 genomes]
rs3774572	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774579	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3774589	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]
rs3774591	0.91[EUR][1000 genomes]
rs4687740	0.94[EUR][1000 genomes]
rs7617553	0.87[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs9881910	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	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
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3821865	TLR9	cis	cerebellum	SCAN
rs3821865	MST1R	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
2	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
3	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:53779000-53806400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:53780400-53807000	Weak transcription	Fetal Brain Female	brain
6	chr3:53781800-53807400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:53785000-53811200	Weak transcription	Spleen	Spleen
8	chr3:53785800-53806600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:53786000-53808200	Weak transcription	Liver	Liver
10	chr3:53788800-53807000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:53789800-53814600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:53796400-53806800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:53796600-53807000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:53796800-53808000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:53798000-53807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:53798400-53804000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:53798800-53807400	Weak transcription	Fetal Brain Male	brain
18	chr3:53799000-53803400	Weak transcription	Lung	lung
19	chr3:53800000-53804800	Weak transcription	Pancreas	Pancrea
20	chr3:53801000-53802800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:53801600-53802400	Enhancers	HepG2	liver
22	chr3:53801800-53802400	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:53801800-53802400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:53801800-53803800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:53801800-53803800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:53801800-53803800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:53802000-53802600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:53802000-53807400	Strong transcription	Fetal Lung	lung
29	chr3:53802200-53802600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:53802200-53803800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:53802200-53807200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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