Variant report

Variant	rs7624039
Chromosome Location	chr3:86685214-86685215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13098318	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201375	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324855	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4270505	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4274747	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4293705	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308277	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345067	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345068	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374531	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624560	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855154	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57429543	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57606469	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800791	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433574	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650493	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877116	chr3:86518318-86964922	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1829775	chr3:86534927-86822085	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv877117	chr3:86665408-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1009339	chr3:86673173-86725713	Weak transcription Enhancers ZNF genes & repeats Active TSS	lncRNA	2 gene(s)	inside rSNPs	n/a
5	esv1794028	chr3:86684769-86822085	Enhancers Active TSS Weak transcription ZNF genes & repeats	lncRNA	11 gene(s)	inside rSNPs	n/a
6	esv1827728	chr3:86684769-86822085	Enhancers Weak transcription ZNF genes & repeats Active TSS	lncRNA	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7624039	PSMD1	cis	Brain Pons	GTEx
rs7624039	ILKAP	cis	Brain Pons	GTEx
rs7624039	APITD1	cis	Brain Pons	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86682200-86685800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:86684000-86685800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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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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