Variant report

Variant	rs7537189
Chromosome Location	chr1:165564845-165564846
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:165564696-165565190	SK-N-SH	brain:	n/a	chr1:165564937-165564944
2	PBX3	chr1:165564711-165565203	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:165564721-165565347	SK-N-SH	brain:	n/a	chr1:165564937-165564944

Variant related genes	Relation type
ENSG00000236206	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10753684	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10800113	0.82[EUR][1000 genomes]
rs10800114	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10800115	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10918219	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918221	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1337441	0.92[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1337444	0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[EUR][1000 genomes]
rs1337448	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1538116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572542	0.90[YRI][hapmap]
rs2138351	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930290	0.89[EUR][1000 genomes]
rs4147592	0.82[YRI][hapmap]
rs4147594	0.82[YRI][hapmap]
rs4147596	0.82[YRI][hapmap]
rs4656450	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657454	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657455	0.87[EUR][1000 genomes]
rs6679871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692834	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543817	0.91[EUR][1000 genomes]
rs7554904	0.82[YRI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7537189	MGST3	cis	Esophagus Mucosa	GTEx
rs7537189	MGST3	Cis_1M	lymphoblastoid	RTeQTL
rs7537189	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	chr1:165562800-165566600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:165564400-165565400	Enhancers	NHDF-Ad	bronchial
4	chr1:165564600-165565200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:165564600-165566600	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:165564800-165565000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:165564800-165565400	Enhancers	HSMM	muscle

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