Variant report

Variant	rs7625470
Chromosome Location	chr3:88959990-88959991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11128061	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12632205	0.82[AMR][1000 genomes]
rs13321295	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483479	0.84[EUR][1000 genomes]
rs1483480	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17026511	0.86[AMR][1000 genomes]
rs35357934	0.82[AMR][1000 genomes]
rs4241402	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4241403	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4301012	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4377496	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4855790	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855806	0.82[AMR][1000 genomes]
rs4855811	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855816	0.92[EUR][1000 genomes]
rs6551368	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6551371	0.84[AMR][1000 genomes]
rs6551372	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6773197	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6792929	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6805311	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7434092	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615019	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7621168	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7630500	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7643228	0.82[AMR][1000 genomes]
rs9284815	0.84[AMR][1000 genomes]
rs9827227	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9830958	0.87[AMR][1000 genomes]
rs9851828	0.86[AMR][1000 genomes]
rs9869106	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9870254	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877157	chr3:88690163-88974863	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv834759	chr3:88901229-89105366	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2763285	chr3:88943041-88985151	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7625470	C3orf38	cis	parietal	SCAN
rs7625470	EPHA3	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88958800-88961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:88959400-88961400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:88959800-88961200	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr3:88959800-88962600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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