Variant report

Variant	rs6782786
Chromosome Location	chr3:179678135-179678136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10804880	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937014	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464783	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534023	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534024	1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037634	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2140654	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2177589	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855126	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855127	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6770184	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775539	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794331	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637321	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637337	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811817	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824233	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825224	0.85[EUR][1000 genomes]
rs9855801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866978	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867274	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6782786	FAM131A	cis	parietal	SCAN
rs6782786	PEX5L	cis	cerebellum	SCAN
rs6782786	FXR1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179660600-179680800	Weak transcription	Pancreas	Pancrea
2	chr3:179672200-179679600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:179675200-179679800	Enhancers	Fetal Thymus	thymus
4	chr3:179675800-179679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:179675800-179688000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:179676400-179678200	Weak transcription	Brain Anterior Caudate	brain
7	chr3:179676600-179678200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:179677200-179678200	Weak transcription	GM12878-XiMat	blood
9	chr3:179677200-179685000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:179677400-179681400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:179677600-179678200	Enhancers	Brain Substantia Nigra	brain
12	chr3:179677800-179678600	Enhancers	Thymus	Thymus
13	chr3:179677800-179681000	Enhancers	Brain Hippocampus Middle	brain
14	chr3:179677800-179681400	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:179678000-179678400	Transcr. at gene 5' and 3'	Dnd41	blood

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