Variant report

Variant	rs563873
Chromosome Location	chr19:39589003-39589004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11882372	0.88[EUR][1000 genomes]
rs1313617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569368	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2569369	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28606601	0.85[EUR][1000 genomes]
rs472265	0.93[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs506417	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs516004	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs565812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs573875	0.81[YRI][hapmap]
rs62119549	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62120479	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62120480	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62120481	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62120482	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62120483	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62120484	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62120485	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62120486	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62120488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62120489	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62120490	0.85[EUR][1000 genomes]
rs692346	0.92[EUR][1000 genomes]
rs692438	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs692461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs692730	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7256505	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7256546	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73045449	0.87[EUR][1000 genomes]
rs774913	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774915	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774916	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774917	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774918	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774919	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774920	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs563873	RSPH6A	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39575800-39601200	Weak transcription	HMEC	breast
2	chr19:39589000-39589200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:39589000-39589400	Bivalent Enhancer	Fetal Intestine Large	intestine
4	chr19:39589000-39589400	Bivalent Enhancer	Fetal Intestine Small	intestine
5	chr19:39589000-39589600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:39589000-39589800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:39589000-39590200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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