Variant report

Variant	rs534757
Chromosome Location	chr15:40226877-40226878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40226656..40228180-chr15:40261724..40263385,2	K562	blood:
2	chr15:40226223..40227908-chr15:40241958..40244363,2	MCF-7	breast:
3	chr15:40226451..40228182-chr15:40236413..40239026,2	MCF-7	breast:
4	chr15:40214834..40219458-chr15:40222098..40228403,10	K562	blood:
5	chr15:40211366..40214080-chr15:40223428..40228644,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259389	Chromatin interaction
ENSG00000166073	Chromatin interaction
ENSG00000238564	Chromatin interaction
ENSG00000200305	Chromatin interaction
ENSG00000246863	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	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656896	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2247984	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412451	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917497	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934194	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs480095	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486816	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489424	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494614	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494690	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500200	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs508281	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518770	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524240	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs525910	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs527610	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535407	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs552251	0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs562159	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]
rs577289	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580836	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs581233	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[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
rs534757	EIF2AK4	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40224800-40227800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:40225200-40227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:40225400-40227000	Active TSS	Brain Substantia Nigra	brain
4	chr15:40225400-40227000	Active TSS	HSMMtube	muscle
5	chr15:40225400-40227400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:40225400-40228000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:40225400-40228200	Active TSS	A549	lung
8	chr15:40225600-40227000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr15:40225600-40227000	Active TSS	Brain Anterior Caudate	brain
10	chr15:40225600-40227000	Active TSS	Stomach Smooth Muscle	stomach
11	chr15:40225600-40227000	Active TSS	NHEK	skin
12	chr15:40225600-40227200	Active TSS	Placenta	Placenta
13	chr15:40225600-40227400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:40225600-40227400	Active TSS	Ovary	ovary
15	chr15:40225600-40227800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:40225600-40227800	Active TSS	HSMM	muscle
17	chr15:40225800-40227000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:40225800-40227000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:40225800-40227000	Active TSS	Fetal Kidney	kidney
20	chr15:40225800-40227000	Active TSS	Fetal Lung	lung
21	chr15:40225800-40227000	Active TSS	Small Intestine	intestine
22	chr15:40225800-40227000	Bivalent/Poised TSS	HepG2	liver
23	chr15:40225800-40227200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr15:40225800-40227200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr15:40225800-40227200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:40225800-40227200	Active TSS	Aorta	Aorta
27	chr15:40225800-40227200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr15:40225800-40227200	Active TSS	Esophagus	oesophagus
29	chr15:40225800-40227200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr15:40225800-40227200	Active TSS	Left Ventricle	heart
31	chr15:40225800-40227200	Active TSS	Lung	lung
32	chr15:40225800-40227200	Active TSS	Pancreas	Pancrea
33	chr15:40225800-40227200	Active TSS	Placenta Amnion	Placenta Amnion
34	chr15:40225800-40227200	Active TSS	Psoas Muscle	Psoas
35	chr15:40225800-40227200	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr15:40225800-40227400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:40225800-40227400	Active TSS	Fetal Brain Female	brain
38	chr15:40225800-40227400	Active TSS	Right Atrium	heart
39	chr15:40225800-40227400	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr15:40225800-40227400	Active TSS	GM12878-XiMat	blood
41	chr15:40225800-40227600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr15:40225800-40227600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:40225800-40227600	Active TSS	NHLF	lung
44	chr15:40225800-40227800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr15:40226000-40227000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:40226000-40227000	Active TSS	Colon Smooth Muscle	Colon
47	chr15:40226000-40227000	Active TSS	Fetal Brain Male	brain
48	chr15:40226000-40227000	Active TSS	Fetal Heart	heart
49	chr15:40226000-40227000	Active TSS	Fetal Intestine Large	intestine
50	chr15:40226000-40227000	Active TSS	Fetal Intestine Small	intestine

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