Variant report

Variant	rs61486548
Chromosome Location	chr2:55173146-55173147
allele	G/T
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	FOS	chr2:55173019-55173216	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:55172975-55173198	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF217	chr2:55172689-55173357	MCF-7	breast:	n/a	n/a
5	MYC	chr2:55172940-55173259	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr2:55173025-55173251	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr2:55172677-55173194	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:55172832-55173252	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr2:55172953-55173268	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr2:55173052-55173219	MCF10A-Er-Src	breast:	n/a	n/a
11	RAD21	chr2:55173098-55173272	IMR90	lung:	n/a	n/a
12	BHLHE40	chr2:55172677-55173209	HepG2	liver:	n/a	n/a
13	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: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10496034	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17046514	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2304687	0.90[AMR][1000 genomes]
rs4233955	0.90[AMR][1000 genomes]
rs4671993	0.90[AMR][1000 genomes]
rs4671995	0.90[AMR][1000 genomes]
rs4671997	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs733916	0.88[AMR][1000 genomes];0.86[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
rs61486548	C2orf73	cis	brain	BrainEAC

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	chr2:55172600-55173200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:55172600-55173200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:55172600-55173200	Enhancers	Right Atrium	heart
16	chr2:55172600-55173400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:55172600-55173400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:55172600-55173600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:55172600-55173600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:55172600-55173600	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:55172600-55173600	Enhancers	Fetal Muscle Trunk	muscle
22	chr2:55172600-55173600	Enhancers	Ovary	ovary
23	chr2:55172600-55173600	Enhancers	Pancreas	Pancrea
24	chr2:55172600-55173600	Enhancers	GM12878-XiMat	blood
25	chr2:55172600-55173600	Enhancers	NHEK	skin
26	chr2:55172600-55173800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:55172600-55173800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:55172600-55173800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55172600-55173800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:55172600-55173800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr2:55172600-55173800	Enhancers	HSMMtube	muscle
32	chr2:55172600-55174000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:55172600-55174000	Enhancers	Fetal Lung	lung
34	chr2:55172600-55174000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr2:55172600-55174200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55172600-55174200	Enhancers	Fetal Brain Female	brain
37	chr2:55172600-55175000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:55172600-55175200	Enhancers	Osteobl	bone
39	chr2:55172600-55176400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:55172800-55173200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr2:55172800-55173200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:55172800-55173200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:55172800-55173200	Enhancers	Esophagus	oesophagus
44	chr2:55172800-55173200	Enhancers	Gastric	stomach
45	chr2:55172800-55173200	Enhancers	Left Ventricle	heart
46	chr2:55172800-55173400	Enhancers	Fetal Stomach	stomach
47	chr2:55172800-55173400	Enhancers	Fetal Thymus	thymus
48	chr2:55172800-55173600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:55172800-55173600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr2:55172800-55173600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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