Variant report

Variant	rs1060455
Chromosome Location	chr19:38850430-38850431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38843850..38848913-chr19:38849820..38852865,6	K562	blood:
2	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
3	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
4	chr19:38849976..38851523-chr19:38865521..38867449,2	MCF-7	breast:
5	chr19:38846299..38848988-chr19:38850348..38854198,4	MCF-7	breast:
6	chr19:38845897..38848818-chr19:38850039..38852720,3	K562	blood:

Variant related genes	Relation type
ENSG00000099338	Chromatin interaction
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11083453	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11878707	1.00[GIH][hapmap]
rs12460181	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12460264	0.83[EUR][1000 genomes]
rs12460599	0.89[AMR][1000 genomes]
rs12461248	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12461700	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12462230	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12463175	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2072350	1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2074979	1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2074980	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2074981	0.81[MEX][hapmap]
rs2286547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2286550	1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2286551	1.00[GIH][hapmap];0.81[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302226	1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35848839	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745956	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745960	1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745961	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745962	1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4802400	0.81[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap]
rs60577771	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60759642	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60915799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61379500	0.93[AMR][1000 genomes];1.00[EUR][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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1060455	FAM98C	cis	multi-tissue	Pritchard
rs1060455	RASGRP4	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
2	chr19:38835200-38852000	Weak transcription	Pancreas	Pancrea
3	chr19:38849400-38851800	Weak transcription	Lung	lung
4	chr19:38850400-38851800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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