Variant report

Variant	rs2227200
Chromosome Location	chr1:172333448-172333449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011731	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1023479	0.95[ASN][1000 genomes]
rs10489284	0.94[ASN][1000 genomes]
rs10752943	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10752944	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10797996	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911654	0.95[ASN][1000 genomes]
rs10911681	0.94[ASN][1000 genomes]
rs10911684	0.92[ASN][1000 genomes]
rs12404665	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12405515	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1894633	0.84[ASN][1000 genomes]
rs2001127	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001128	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213731	0.92[ASN][1000 genomes]
rs2213732	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227198	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2227199	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269612	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301453	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213564	0.95[ASN][1000 genomes]
rs3768445	0.92[ASN][1000 genomes]
rs4471302	0.94[ASN][1000 genomes]
rs4504922	0.94[ASN][1000 genomes]
rs4916251	0.95[ASN][1000 genomes]
rs4916252	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916253	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916254	0.85[ASN][1000 genomes]
rs57668887	0.82[ASN][1000 genomes]
rs6424894	0.92[ASN][1000 genomes]
rs6676665	0.92[ASN][1000 genomes]
rs6697844	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6698987	0.90[ASN][1000 genomes]
rs6700575	0.94[ASN][1000 genomes]
rs714515	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73046851	0.82[ASN][1000 genomes]
rs7517737	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518039	0.92[ASN][1000 genomes]
rs7534393	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7539464	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539972	0.92[ASN][1000 genomes]
rs7544610	0.92[ASN][1000 genomes]
rs7546252	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9286854	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425291	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9425297	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425298	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425299	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425300	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425301	0.94[ASN][1000 genomes]
rs9425568	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9425573	0.84[ASN][1000 genomes]
rs9425575	0.82[ASN][1000 genomes]
rs9425579	0.94[ASN][1000 genomes]
rs9425586	0.95[ASN][1000 genomes]
rs9425587	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425589	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425590	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425591	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9425592	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs979935	0.82[ASN][1000 genomes]
rs991790	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3543	chr1:172323563-172334586	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2227200	PIGC	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172328400-172334000	Weak transcription	Aorta	Aorta
2	chr1:172329200-172334600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:172329800-172334000	Weak transcription	Left Ventricle	heart
4	chr1:172329800-172334000	Weak transcription	Osteobl	bone
5	chr1:172330400-172336600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:172330400-172343000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:172331000-172336400	Weak transcription	Small Intestine	intestine
8	chr1:172331200-172347200	Weak transcription	Fetal Kidney	kidney
9	chr1:172332200-172334800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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