Variant report

Variant	rs3821860
Chromosome Location	chr3:53779825-53779826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53777857..53780018-chr3:53784994..53786883,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11719163	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11918583	0.96[CEU][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs1380612	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1401497	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs28365115	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28434705	0.87[EUR][1000 genomes]
rs3733070	0.88[EUR][1000 genomes]
rs3774563	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3774567	0.86[EUR][1000 genomes]
rs3774570	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs3774577	1.00[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3774580	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs3821866	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs3846215	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41276449	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56384446	0.85[EUR][1000 genomes]
rs6776947	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs6797014	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs714786	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9311514	0.96[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3821860	NPRL2	cis	parietal	SCAN
rs3821860	ACTR8	cis	parietal	SCAN
rs3821860	RBM5	cis	parietal	SCAN
rs3821860	PDE12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
2	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
4	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:53766600-53781200	Weak transcription	Lung	lung
7	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
8	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
10	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
11	chr3:53774400-53782000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:53774600-53785000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
14	chr3:53777800-53787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:53778400-53781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:53778400-53781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:53778800-53781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:53778800-53781800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:53778800-53781800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:53778800-53783800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:53778800-53797000	Weak transcription	Pancreas	Pancrea
23	chr3:53779000-53781800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:53779000-53784000	Weak transcription	Fetal Thymus	thymus
25	chr3:53779000-53806400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:53779400-53787800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:53779800-53780600	Strong transcription	Liver	Liver
28	chr3:53779800-53780600	Weak transcription	GM12878-XiMat	blood
29	chr3:53779800-53781600	Strong transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:53779800-53781800	Strong transcription	Brain Anterior Caudate	brain
31	chr3:53779800-53788800	Strong transcription	Brain Inferior Temporal Lobe	brain

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