Variant report

Variant	rs4504034
Chromosome Location	chr2:55173226-55173227
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:55172594-55173269	IMR90	lung:	n/a	n/a
2	ZNF217	chr2:55172689-55173357	MCF-7	breast:	n/a	n/a
3	MYC	chr2:55172940-55173259	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:55173025-55173251	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr2:55172832-55173252	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr2:55172953-55173268	MCF10A-Er-Src	breast:	n/a	n/a
7	RAD21	chr2:55173098-55173272	IMR90	lung:	n/a	n/a
8	CEBPB	chr2:55172900-55173370	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55171297..55173305-chr2:55180645..55183398,2	K562	blood:
2	chr2:39442463..39443026-chr2:55172640..55173316,2	MCF-7	breast:
3	chr15:90568357..90570526-chr2:55172089..55173609,2	MCF-7	breast:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10196667	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198636	0.87[EUR][1000 genomes]
rs10746530	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125551	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11904457	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12475185	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13008105	0.97[ASN][1000 genomes]
rs13020490	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13026576	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13028800	0.97[ASN][1000 genomes]
rs17418111	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2304685	0.84[AMR][1000 genomes]
rs36024305	0.97[ASN][1000 genomes]
rs36063689	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4233956	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4525735	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671233	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4671998	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55777421	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6545462	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67721747	0.84[AMR][1000 genomes];0.97[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv3393792	chr2:55171448-55173496	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4504034	RTN4	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55172200-55174200	Enhancers	Brain Hippocampus Middle	brain
4	chr2:55172400-55173800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:55172400-55173800	Enhancers	HMEC	breast
6	chr2:55172400-55173800	Enhancers	NHLF	lung
7	chr2:55172400-55174000	Enhancers	NHDF-Ad	bronchial
8	chr2:55172400-55174200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:55172400-55174400	Enhancers	Brain Angular Gyrus	brain
10	chr2:55172400-55175400	Enhancers	Fetal Brain Male	brain
11	chr2:55172400-55175600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:55172400-55176000	Enhancers	Fetal Muscle Leg	muscle
13	chr2:55172600-55173400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:55172600-55173400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:55172600-55173600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:55172600-55173600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55172600-55173600	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:55172600-55173600	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:55172600-55173600	Enhancers	Ovary	ovary
20	chr2:55172600-55173600	Enhancers	Pancreas	Pancrea
21	chr2:55172600-55173600	Enhancers	GM12878-XiMat	blood
22	chr2:55172600-55173600	Enhancers	NHEK	skin
23	chr2:55172600-55173800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55172600-55173800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:55172600-55173800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:55172600-55173800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:55172600-55173800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:55172600-55173800	Enhancers	HSMMtube	muscle
29	chr2:55172600-55174000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:55172600-55174000	Enhancers	Fetal Lung	lung
31	chr2:55172600-55174000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr2:55172600-55174200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:55172600-55174200	Enhancers	Fetal Brain Female	brain
34	chr2:55172600-55175000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:55172600-55175200	Enhancers	Osteobl	bone
36	chr2:55172600-55176400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:55172800-55173400	Enhancers	Fetal Stomach	stomach
38	chr2:55172800-55173400	Enhancers	Fetal Thymus	thymus
39	chr2:55172800-55173600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:55172800-55173600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr2:55172800-55173600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:55172800-55173600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr2:55172800-55173600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:55172800-55173600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:55172800-55173600	Enhancers	Placenta	Placenta
46	chr2:55172800-55173600	Enhancers	Lung	lung
47	chr2:55172800-55173800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr2:55172800-55174200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:55172800-55174400	Enhancers	Brain Germinal Matrix	brain
50	chr2:55172800-55175800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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