Variant report

Variant	rs1572542
Chromosome Location	chr1:165550009-165550010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10737514	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10753683	0.97[ASN][1000 genomes]
rs10918207	0.81[YRI][hapmap]
rs10918216	0.98[ASN][1000 genomes]
rs10918217	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918218	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12025040	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1326376	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1425754	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1572541	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]
rs2433137	0.83[MEX][hapmap]
rs6657863	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs722259	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7537189	0.90[YRI][hapmap]
rs7554904	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv946479	chr1:165549846-165553079	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1572542	MGST3	cis	lymphoblastoid	seeQTL
rs1572542	C1orf192	cis	cerebellum	SCAN
rs1572542	ILDR2	cis	parietal	SCAN
rs1572542	IGSF8	cis	parietal	SCAN
rs1572542	MGST3	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165547400-165566800	Weak transcription	Psoas Muscle	Psoas
2	chr1:165549000-165551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:165549600-165551200	Enhancers	NHEK	skin
4	chr1:165549600-165551600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:165549600-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:165549800-165551600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:165550000-165550200	Enhancers	Placenta	Placenta

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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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