Variant report

Variant	rs60313653
Chromosome Location	chr15:39706723-39706724
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39704919..39707647-chr20:52293554..52295684,2	MCF-7	breast:
2	chr15:39705799..39707909-chr15:39873297..39874835,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10520131	0.82[ASN][1000 genomes]
rs11630143	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630296	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631131	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631290	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631466	0.95[EUR][1000 genomes]
rs11631836	0.90[EUR][1000 genomes]
rs11634087	0.95[EUR][1000 genomes]
rs11634167	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11634541	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634743	0.86[ASN][1000 genomes]
rs11635229	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635586	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636438	0.95[EUR][1000 genomes]
rs11637421	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16952114	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16952143	0.86[ASN][1000 genomes]
rs16952145	0.86[ASN][1000 genomes]
rs16952153	0.86[ASN][1000 genomes]
rs16969090	0.86[ASN][1000 genomes]
rs16969092	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969119	0.86[EUR][1000 genomes]
rs1973175	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3960597	1.00[EUR][1000 genomes]
rs3973348	1.00[EUR][1000 genomes]
rs3973349	1.00[EUR][1000 genomes]
rs3973365	0.95[EUR][1000 genomes]
rs4603529	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55848083	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56313937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56329829	0.86[ASN][1000 genomes]
rs58157051	0.86[ASN][1000 genomes]
rs58280064	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60266259	0.86[ASN][1000 genomes]
rs60420802	0.86[ASN][1000 genomes]
rs60623717	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60664658	0.95[EUR][1000 genomes]
rs61545963	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165434	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7166266	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7171447	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7171799	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174276	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73393456	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73393472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399395	0.86[EUR][1000 genomes]
rs74010136	0.86[ASN][1000 genomes]
rs8042191	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60313653	EIF2AK4	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39700000-39707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:39703200-39708000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:39703200-39708600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:39703800-39706800	Weak transcription	HepG2	liver
5	chr15:39704200-39708400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr15:39704200-39718800	Weak transcription	Thymus	Thymus
7	chr15:39704600-39707200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:39705000-39707200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:39705400-39706800	Enhancers	NHDF-Ad	bronchial
10	chr15:39705400-39708600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:39705600-39708800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr15:39705800-39707000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:39706000-39707400	Enhancers	Primary hematopoietic stem cells	blood
14	chr15:39706200-39712000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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