Variant report

Variant	rs11799903
Chromosome Location	chr1:165592533-165592534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165589382..165593490-chr1:165595077..165601598,7	K562	blood:
2	chr1:165590538..165593490-chr1:165599328..165601598,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGST3-1	chr1:165592482-165592568	ENSG00000236206
2	lnc-MGST3-1	chr1:165592482-165592568	NONHSAT007321

Variant related genes	Relation type
ENSG00000143198	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11799886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11801981	1.00[JPT][hapmap]
rs11806754	1.00[JPT][hapmap]
rs11808590	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11809495	0.93[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11809976	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1415500	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1415501	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1415502	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs16847487	1.00[JPT][hapmap]
rs16847544	1.00[JPT][hapmap]
rs1832296	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1913838	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs28682307	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4504864	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs57098971	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs57831387	0.96[EUR][1000 genomes]
rs57947536	0.97[EUR][1000 genomes]
rs58754537	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs60755789	0.97[EUR][1000 genomes]
rs6426921	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6426923	0.98[EUR][1000 genomes]
rs6426924	0.99[EUR][1000 genomes]
rs6669092	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6679779	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6682771	1.00[JPT][hapmap]
rs6686643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6689822	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6689895	0.99[EUR][1000 genomes]
rs6689903	0.93[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6689926	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6690104	0.99[EUR][1000 genomes]
rs6690679	0.93[CEU][hapmap];0.99[EUR][1000 genomes]
rs6693448	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6693471	0.99[EUR][1000 genomes]
rs6695758	1.00[JPT][hapmap]
rs6701006	1.00[CEU][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6703260	0.99[EUR][1000 genomes]
rs7516587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7537008	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7537273	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7537321	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7537398	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7548938	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7548946	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7554034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9333378	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9333433	1.00[CHB][hapmap]
rs9333461	0.83[ASN][1000 genomes]
rs9333464	1.00[JPT][hapmap]
rs9333471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs959617	1.00[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11799903	MGST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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