Variant report

Variant	rs10800114
Chromosome Location	chr1:165572150-165572151
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000224358	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10753684	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800113	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10800115	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918219	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918221	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133779	0.87[ASN][1000 genomes]
rs1337441	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1337444	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1337448	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538116	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2138351	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3930290	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656450	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657454	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657455	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679871	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6692834	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7537189	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7543817	0.88[EUR][1000 genomes];0.93[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	nsv429902	chr1:165531342-165574342	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10800114	MGST3	cis	multi-tissue	Pritchard
rs10800114	ILDR2	cis	parietal	SCAN
rs10800114	MGST3	cis	lymphoblastoid	seeQTL
rs10800114	B4GALT3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165568000-165572800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:165568000-165574800	Weak transcription	Right Atrium	heart
3	chr1:165568200-165579600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:165571000-165572600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:165571400-165573000	Weak transcription	Liver	Liver
6	chr1:165571400-165573000	Weak transcription	HepG2	liver

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Input of quick search could be:

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

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