Variant report

Variant	rs1572541
Chromosome Location	chr1:165549624-165549625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10737514	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10753683	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918217	1.00[ASN][1000 genomes]
rs10918218	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12025040	0.96[ASN][1000 genomes]
rs1326376	0.98[ASN][1000 genomes]
rs1425754	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1572542	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs1913841	0.84[EUR][1000 genomes]
rs2766081	0.93[EUR][1000 genomes]
rs367199	0.95[CEU][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs369598	0.93[EUR][1000 genomes]
rs453717	0.93[EUR][1000 genomes]
rs6657863	0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap]
rs722259	0.94[ASN][1000 genomes]
rs7554904	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1572541	MGST3	cis	parietal	SCAN
rs1572541	KCNJ9	cis	parietal	SCAN
rs1572541	CASQ1	cis	cerebellum	SCAN
rs1572541	C1orf110	cis	parietal	SCAN
rs1572541	MGST3	cis	lymphoblastoid	seeQTL
rs1572541	MGST3	Cis_1M	lymphoblastoid	RTeQTL
rs1572541	ILDR2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165547400-165549800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:165547400-165566800	Weak transcription	Psoas Muscle	Psoas
3	chr1:165549000-165551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:165549600-165551200	Enhancers	NHEK	skin
5	chr1:165549600-165551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:165549600-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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