Variant report

Variant	rs3774580
Chromosome Location	chr3:53802629-53802630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1045958	0.82[ASW][hapmap]
rs11719163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918583	1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17053472	0.84[GIH][hapmap]
rs28365115	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28434705	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343863	0.80[EUR][1000 genomes]
rs3733070	0.88[EUR][1000 genomes]
rs3774567	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3774570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774577	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821860	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs3821866	0.95[CEU][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3846215	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276449	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56384446	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6776947	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797014	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311514	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809645	1.00[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3774580	ACTR8	cis	parietal	SCAN
rs3774580	NPRL2	cis	parietal	SCAN
rs3774580	PDE12	cis	parietal	SCAN
rs3774580	RBM5	cis	parietal	SCAN

Chromatin state (count:32 , 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	chr3:53801800-53803800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:53801800-53803800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:53801800-53803800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:53802000-53807400	Strong transcription	Fetal Lung	lung
25	chr3:53802200-53803800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:53802200-53807200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:53802400-53807000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:53802400-53818200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:53802600-53803600	Enhancers	Fetal Heart	heart
30	chr3:53802600-53803600	Enhancers	Fetal Thymus	thymus
31	chr3:53802600-53803800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:53802600-53804200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links