Variant report

Variant	rs171748
Chromosome Location	chr5:60499131-60499132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10939886	0.82[ASN][1000 genomes]
rs159360	0.82[ASN][1000 genomes]
rs159365	0.86[EUR][1000 genomes]
rs159538	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159539	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159540	0.83[AFR][1000 genomes]
rs159542	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs194369	1.00[ASN][1000 genomes]
rs34627	0.82[ASN][1000 genomes]
rs34631	0.82[ASN][1000 genomes]
rs34634	0.98[ASN][1000 genomes]
rs34635	0.81[EUR][1000 genomes]
rs40506	0.82[ASN][1000 genomes]
rs476099	0.82[ASN][1000 genomes]
rs6864095	0.81[ASN][1000 genomes]
rs6864489	0.81[ASN][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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	esv1845980	chr5:60481408-60511495	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	23974872	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs171748	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60497000-60499200	Enhancers	Osteobl	bone
2	chr5:60497000-60499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:60499000-60499200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:60499000-60499400	Weak transcription	HSMM	muscle

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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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