Variant report

Variant	rs482679
Chromosome Location	chr19:39557880-39557881
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10407957	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10408661	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12151180	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569365	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34738600	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377373	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380679	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384605	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs385681	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs392005	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs392135	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs393559	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs395387	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs396616	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs397189	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs400011	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs420682	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426076	0.95[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs452666	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs453853	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4802015	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4803196	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803197	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487456	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs578940	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs597995	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs602744	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs620642	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621580	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648192	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs648635	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs665998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690812	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691059	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs691114	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs691266	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs691391	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691890	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692294	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs692343	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs692347	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs774727	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs774927	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs774928	0.93[AMR][1000 genomes];0.98[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	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv522530	chr19:39552150-39573918	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs482679	KCNN4	cis	cerebellum	SCAN
rs482679	TGFB1	cis	parietal	SCAN
rs482679	GIPR	cis	parietal	SCAN
rs482679	PSG3	cis	parietal	SCAN
rs482679	PVRL2	cis	parietal	SCAN
rs482679	LYPD3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39545200-39564400	Weak transcription	Brain Substantia Nigra	brain
2	chr19:39545600-39560400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:39549800-39558800	Weak transcription	Right Atrium	heart
4	chr19:39555800-39558800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:39556000-39560400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:39556000-39561000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:39557000-39558200	Enhancers	HepG2	liver
8	chr19:39557000-39564400	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:39557200-39561200	Weak transcription	Brain Inferior Temporal Lobe	brain

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