Variant report

Variant	rs7307979
Chromosome Location	chr12:56040682-56040683
allele	C/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	E2F6	chr12:56039886-56040806	H1-hESC	embryonic stem cell:	n/a	chr12:56040133-56040142 chr12:56040595-56040607
2	MTA3	chr12:56039855-56040769	GM12878	blood:	n/a	n/a
3	ELF1	chr12:56039763-56040769	GM12878	blood:	n/a	chr12:56039998-56040007 chr12:56039997-56040008
4	CTCF	chr12:56039767-56040757	SK-N-SH	brain:	n/a	chr12:56040092-56040110 chr12:56040093-56040109
5	CTCF	chr12:56039635-56040692	HCT-116	colon:	n/a	chr12:56040092-56040110 chr12:56040093-56040109
6	NRF1	chr12:56039912-56040793	SK-N-SH	brain:	n/a	chr12:56040132-56040143 chr12:56040129-56040143 chr12:56040132-56040141 chr12:56040131-56040142
7	E2F6	chr12:56039938-56040879	H1-hESC	embryonic stem cell:	n/a	chr12:56040133-56040142 chr12:56040595-56040607
8	MAX	chr12:56039864-56040785	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56040086..56042095-chr12:56114770..56116489,2	MCF-7	breast:
2	chr12:55552029..55554252-chr12:56038940..56041614,2	MCF-7	breast:
3	chr12:55561734..55564390-chr12:56040616..56042476,2	K562	blood:

Variant related genes	Relation type
OR10AE3P	TF binding region
ENSG00000224622	Chromatin interaction
ENSG00000135437	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10783764	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474447	0.97[ASN][1000 genomes]
rs2555034	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2555035	0.87[ASN][1000 genomes]
rs2694014	0.97[ASN][1000 genomes]
rs3953273	0.97[ASN][1000 genomes]
rs4387385	0.82[ASN][1000 genomes]
rs4759183	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6581075	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7133382	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7295016	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965259	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv559001	chr12:55507465-56057708	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56033800-56041400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:56039200-56041200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:56039800-56040800	Enhancers	Fetal Thymus	thymus
4	chr12:56039800-56041200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:56040000-56040800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:56040200-56040800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:56040200-56040800	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:56040200-56040800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr12:56040200-56040800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr12:56040200-56040800	Enhancers	Stomach Mucosa	stomach
11	chr12:56040200-56040800	Enhancers	HUVEC	blood vessel
12	chr12:56040200-56040800	Flanking Active TSS	K562	blood
13	chr12:56040200-56041000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:56040200-56041000	Enhancers	Gastric	stomach
15	chr12:56040200-56041200	Enhancers	Lung	lung
16	chr12:56040400-56040800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr12:56040400-56040800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr12:56040400-56040800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:56040400-56040800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:56040400-56040800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:56040400-56040800	Enhancers	Brain Substantia Nigra	brain
22	chr12:56040400-56040800	Enhancers	Placenta	Placenta
23	chr12:56040400-56040800	Enhancers	Spleen	Spleen
24	chr12:56040400-56040800	Enhancers	GM12878-XiMat	blood
25	chr12:56040400-56041000	Enhancers	Primary B cells from peripheral blood	blood
26	chr12:56040400-56041000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:56040400-56041000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr12:56040400-56041200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:56040400-56048400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:56040600-56040800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr12:56040600-56040800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr12:56040600-56040800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:56040600-56040800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:56040600-56040800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr12:56040600-56040800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr12:56040600-56040800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr12:56040600-56040800	Enhancers	Colonic Mucosa	Colon
38	chr12:56040600-56040800	Enhancers	Duodenum Mucosa	Duodenum
39	chr12:56040600-56040800	Enhancers	Right Ventricle	heart
40	chr12:56040600-56040800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr12:56040600-56040800	Enhancers	HepG2	liver
42	chr12:56040600-56041000	Enhancers	Adipose Nuclei	Adipose
43	chr12:56040600-56041000	Enhancers	Left Ventricle	heart
44	chr12:56040600-56041000	Enhancers	Pancreas	Pancrea
45	chr12:56040600-56041200	Enhancers	Right Atrium	heart
46	chr12:56040600-56041400	Enhancers	Fetal Muscle Leg	muscle
47	chr12:56040600-56041600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr12:56040600-56041800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:56040600-56042600	Weak transcription	Fetal Intestine Small	intestine
50	chr12:56040600-56043000	Weak transcription	H9 Cell Line	embryonic stem cell

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