Variant report

Variant	rs159540
Chromosome Location	chr5:60484660-60484661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60483051..60485415-chr5:60488357..60490268,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10044518	1.00[JPT][hapmap]
rs10044575	1.00[JPT][hapmap]
rs12186613	0.88[ASN][1000 genomes]
rs12188621	1.00[JPT][hapmap]
rs12188882	1.00[JPT][hapmap]
rs12516321	0.87[CEU][hapmap]
rs159366	0.81[EUR][1000 genomes]
rs159368	0.82[EUR][1000 genomes]
rs159373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs159379	0.88[ASN][1000 genomes]
rs159539	0.83[AFR][1000 genomes]
rs159542	0.82[AFR][1000 genomes]
rs171748	0.83[AFR][1000 genomes]
rs1841504	0.88[ASN][1000 genomes]
rs2545476	0.88[ASN][1000 genomes]
rs256373	0.82[EUR][1000 genomes]
rs2613632	0.88[ASN][1000 genomes]
rs295523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295547	0.92[ASN][1000 genomes]
rs295548	0.92[ASN][1000 genomes]
rs295549	0.92[ASN][1000 genomes]
rs295550	0.83[ASN][1000 genomes]
rs295568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295570	0.88[ASN][1000 genomes]
rs295572	0.88[ASN][1000 genomes]
rs295574	0.88[ASN][1000 genomes]
rs295576	0.88[ASN][1000 genomes]
rs295577	0.88[ASN][1000 genomes]
rs295580	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs295581	0.88[ASN][1000 genomes]
rs298624	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs298625	0.88[ASN][1000 genomes]
rs298626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298630	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs298631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4256302	1.00[JPT][hapmap]
rs498497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs557092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs603018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs159540	ERCC8	cis	lymphoblastoid	seeQTL
rs159540	ERCC8	cis	multi-tissue	Pritchard
rs159540	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs159540	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60483800-60484800	Enhancers	Right Atrium	heart
2	chr5:60484200-60486600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:60484200-60486600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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