Variant report

Variant	rs1418433
Chromosome Location	chr6:44752568-44752569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1022730	0.86[ASN][1000 genomes]
rs1022731	0.86[ASN][1000 genomes]
rs10948187	0.80[TSI][hapmap]
rs10948190	0.80[TSI][hapmap]
rs12215252	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1338907	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1342640	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1832897	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980265	0.80[TSI][hapmap]
rs2145826	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227831	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs227837	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs227838	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs227841	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs227843	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs227847	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs227848	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227849	0.93[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs227850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs227854	0.90[JPT][hapmap]
rs227855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3778507	0.80[TSI][hapmap]
rs3799968	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs494982	0.80[TSI][hapmap]
rs636845	0.80[TSI][hapmap]
rs6458412	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910294	0.85[CEU][hapmap]
rs911524	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349303	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9369514	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs9369515	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9369516	0.80[TSI][hapmap]
rs9369523	0.95[CHB][hapmap]
rs9395051	0.80[TSI][hapmap]
rs9472339	0.91[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1418433	SUPT3H	cis	lymphoblastoid	seeQTL
rs1418433	C6orf226	cis	cerebellum	SCAN
rs1418433	SUPT3H	cis	multi-tissue	Pritchard
rs1418433	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs1418433	SUPT3H	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44751000-44752800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:44752000-44752800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:44752400-44753000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:44752400-44753200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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