Variant report

Variant	rs562159
Chromosome Location	chr15:40218971-40218972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40214834..40219458-chr15:40222098..40228403,10	K562	blood:
2	chr15:40218686..40222213-chr15:40224806..40227355,3	MCF-7	breast:
3	chr15:40180749..40182954-chr15:40217728..40220532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10518676	0.84[JPT][hapmap]
rs10851392	0.82[JPT][hapmap]
rs11633416	0.84[JPT][hapmap]
rs12324733	0.82[JPT][hapmap]
rs12439335	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs1656894	0.87[ASN][1000 genomes]
rs1656895	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656896	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2247984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412451	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917497	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934194	0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs480095	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489424	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494690	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500200	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs508281	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518770	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524240	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs525910	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs527610	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534757	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535407	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs552251	0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs577289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580836	0.84[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs581233	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030025	0.84[JPT][hapmap]
rs8030687	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs562159	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40213600-40225000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:40213600-40225400	Weak transcription	Pancreas	Pancrea
3	chr15:40213800-40225800	Weak transcription	Right Atrium	heart
4	chr15:40215200-40226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:40215600-40225800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:40218200-40224800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:40218200-40225000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:40218400-40224200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:40218400-40224800	Weak transcription	Hela-S3	cervix
10	chr15:40218800-40219000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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