Variant report

Variant	rs73300689
Chromosome Location	chr12:48109624-48109625
allele	C/G
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	FOS	chr12:48109122-48109735	MCF10A-Er-Src	breast:	n/a	chr12:48109399-48109413
2	CTCF	chr12:48108763-48109689	A549	lung:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
3	FOS	chr12:48109296-48109762	MCF10A-Er-Src	breast:	n/a	chr12:48109399-48109413
4	CTCF	chr12:48109540-48109690	GM12866	blood:	n/a	n/a
5	CTCF	chr12:48108901-48109873	HCT-116	colon:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
6	RAD21	chr12:48108901-48109738	HCT-116	colon:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
7	STAT3	chr12:48109249-48109829	MCF10A-Er-Src	breast:	n/a	chr12:48109753-48109765
8	STAT3	chr12:48109268-48109828	MCF10A-Er-Src	breast:	n/a	chr12:48109753-48109765
9	E2F4	chr12:48109314-48109782	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr12:48109560-48109710	Caco-2	colon:	n/a	n/a
11	POLR2A	chr12:48109393-48109691	MCF10A-Er-Src	breast:	n/a	n/a
12	RAD21	chr12:48108961-48109630	MCF-7	breast:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
13	RAD21	chr12:48108959-48109798	SK-N-SH	brain:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
14	STAT3	chr12:48109040-48109761	MCF10A-Er-Src	breast:	n/a	n/a
15	RAD21	chr12:48108846-48109677	HCT-116	colon:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
16	RAD21	chr12:48108971-48109714	ECC-1	luminal epithelium:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
17	RAD21	chr12:48109052-48109666	IMR90	lung:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
18	RAD21	chr12:48108971-48109630	A549	lung:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
19	FOS	chr12:48109345-48109737	MCF10A-Er-Src	breast:	n/a	chr12:48109399-48109413
20	CTCF	chr12:48109520-48109670	HAc	cerebellar:	n/a	n/a
21	ZNF263	chr12:48109131-48110377	HEK293-T-REx	kidney:	n/a	chr12:48109667-48109676
22	MYC	chr12:48109394-48109675	MCF10A-Er-Src	breast:	n/a	n/a
23	MYC	chr12:48109350-48109695	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr12:48109354-48109802	MCF10A-Er-Src	breast:	n/a	chr12:48109753-48109765
25	SMC3	chr12:48108668-48109760	SK-N-SH	brain:	n/a	chr12:48109264-48109274 chr12:48109260-48109274
26	CTCF	chr12:48108771-48110151	SK-N-SH	brain:	n/a	chr12:48109258-48109276 chr12:48109887-48109900 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
27	NFIC	chr12:48109028-48109666	ECC-1	luminal epithelium:	n/a	n/a
28	RAD21	chr12:48109015-48109646	A549	lung:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
29	FOS	chr12:48109395-48109725	MCF10A-Er-Src	breast:	n/a	chr12:48109399-48109413

No.	Distal block	Cell Line	Cell type
1	chr12:48109201..48109826-chr12:48152830..48153420,3	K562	blood:
2	chr12:48108686..48109785-chr12:48232014..48233018,9	MCF-7	breast:
3	chr12:48107776..48110722-chr12:48159579..48161577,2	K562	blood:
4	chr12:48108449..48110795-chr12:48232871..48234613,2	K562	blood:
5	chr12:48109315..48109818-chr12:48227458..48228193,2	K562	blood:
6	chr12:48108810..48109754-chr12:48172755..48173734,6	K562	blood:
7	chr12:48109150..48109703-chr12:48135845..48136359,2	MCF-7	breast:
8	chr12:48109273..48110145-chr12:48132178..48132996,2	K562	blood:
9	chr12:48109020..48109676-chr12:48117627..48118375,2	K562	blood:
10	chr12:48109212..48111939-chr12:48164649..48166863,2	MCF-7	breast:
11	chr12:48108711..48109786-chr12:48173181..48173711,3	MCF-7	breast:
12	chr12:48108161..48111101-chr12:48229795..48232541,2	K562	blood:
13	chr12:48108886..48110989-chr12:48118546..48121224,2	MCF-7	breast:
14	chr12:48108894..48109761-chr12:48170471..48172411,6	K562	blood:
15	chr12:48108886..48109697-chr12:48230502..48231168,3	K562	blood:
16	chr12:48108739..48111513-chr12:48143992..48146721,2	MCF-7	breast:
17	chr12:48108762..48109744-chr12:48166665..48167534,3	MCF-7	breast:
18	chr12:48108819..48109771-chr12:48342972..48343902,5	K562	blood:
19	chr12:48109596..48111288-chr12:48213761..48215553,2	MCF-7	breast:
20	chr12:48109272..48110137-chr12:48166888..48167537,3	MCF-7	breast:
21	chr12:48108819..48109698-chr12:48232035..48232888,2	MCF-7	breast:
22	chr12:48107756..48109662-chr12:48167416..48168986,2	K562	blood:
23	chr12:48108389..48110707-chr12:48231215..48233864,2	MCF-7	breast:
24	chr12:48108347..48109699-chr12:48160633..48161575,5	K562	blood:
25	chr12:48109324..48111684-chr12:48163704..48166114,2	K562	blood:
26	chr12:48108354..48111166-chr12:48231258..48232998,20	K562	blood:
27	chr12:48098499..48101428-chr12:48108711..48111511,2	MCF-7	breast:
28	chr12:48109034..48109734-chr12:48167005..48167508,2	K562	blood:
29	chr12:48108589..48112284-chr12:48169450..48173129,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257433	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000257433	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1859256	1.00[AMR][1000 genomes]
rs57162394	1.00[AMR][1000 genomes]
rs57691959	1.00[AMR][1000 genomes]
rs57848393	0.87[AFR][1000 genomes]
rs58237186	1.00[AMR][1000 genomes]
rs58280987	1.00[AMR][1000 genomes]
rs58348653	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58350284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58636268	1.00[AMR][1000 genomes]
rs59421933	1.00[AMR][1000 genomes]
rs60045275	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60608560	1.00[AMR][1000 genomes]
rs61033936	1.00[AMR][1000 genomes]
rs61288073	1.00[AMR][1000 genomes]
rs61327127	1.00[AMR][1000 genomes]
rs61446607	1.00[AMR][1000 genomes]
rs61734364	1.00[AMR][1000 genomes]
rs61739888	1.00[AMR][1000 genomes]
rs67201012	0.87[AFR][1000 genomes]
rs67408202	0.87[AFR][1000 genomes]
rs7300107	1.00[AMR][1000 genomes]
rs7314320	1.00[AMR][1000 genomes]
rs73300649	1.00[AMR][1000 genomes]
rs73300701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302603	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302628	1.00[AMR][1000 genomes]
rs73302629	1.00[AMR][1000 genomes]
rs73302650	1.00[AMR][1000 genomes]
rs73302653	1.00[AMR][1000 genomes]
rs73302662	1.00[AMR][1000 genomes]
rs73302664	1.00[AMR][1000 genomes]
rs73302673	1.00[AMR][1000 genomes]
rs73302677	1.00[AMR][1000 genomes]
rs73302679	1.00[AMR][1000 genomes]
rs73302681	1.00[AMR][1000 genomes]
rs73302682	1.00[AMR][1000 genomes]
rs757283	1.00[AMR][1000 genomes]
rs7965816	1.00[AMR][1000 genomes]
rs877196	1.00[AMR][1000 genomes]
rs877197	1.00[AMR][1000 genomes]
rs877198	1.00[AMR][1000 genomes]
rs879177	1.00[AMR][1000 genomes]
rs879178	1.00[AMR][1000 genomes]
rs879179	1.00[AMR][1000 genomes]
rs9738787	1.00[AMR][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	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48100000-48111200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48101400-48111000	Weak transcription	Colonic Mucosa	Colon
3	chr12:48101400-48111200	Weak transcription	Small Intestine	intestine
4	chr12:48101800-48111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:48102800-48125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:48103200-48111200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:48103400-48111000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:48104600-48113000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:48105600-48111200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:48106200-48112600	Enhancers	Ovary	ovary
11	chr12:48106600-48111200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:48108200-48112400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:48108600-48112400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr12:48108800-48109800	Enhancers	Fetal Lung	lung
15	chr12:48108800-48111200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr12:48108800-48111200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr12:48108800-48112200	Enhancers	Brain Angular Gyrus	brain
18	chr12:48108800-48112200	Enhancers	Fetal Muscle Trunk	muscle
19	chr12:48108800-48112600	Enhancers	Brain Cingulate Gyrus	brain
20	chr12:48108800-48112600	Enhancers	Fetal Muscle Leg	muscle
21	chr12:48108800-48112600	Enhancers	Fetal Stomach	stomach
22	chr12:48108800-48112600	Enhancers	Left Ventricle	heart
23	chr12:48108800-48112600	Enhancers	Right Atrium	heart
24	chr12:48108800-48112600	Enhancers	Right Ventricle	heart
25	chr12:48108800-48112800	Enhancers	Brain Hippocampus Middle	brain
26	chr12:48108800-48112800	Enhancers	Brain Substantia Nigra	brain
27	chr12:48108800-48113000	Enhancers	Rectal Smooth Muscle	rectum
28	chr12:48109000-48109800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:48109000-48109800	Enhancers	Aorta	Aorta
30	chr12:48109000-48109800	Enhancers	Duodenum Mucosa	Duodenum
31	chr12:48109000-48109800	Enhancers	Fetal Intestine Large	intestine
32	chr12:48109000-48109800	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr12:48109000-48109800	Enhancers	Thymus	Thymus
34	chr12:48109000-48109800	Enhancers	NH-A	brain
35	chr12:48109000-48110000	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:48109000-48110000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr12:48109000-48110000	Enhancers	Pancreas	Pancrea
38	chr12:48109000-48110200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:48109000-48110200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:48109000-48110200	Enhancers	Fetal Heart	heart
41	chr12:48109000-48110200	Enhancers	Stomach Mucosa	stomach
42	chr12:48109000-48110200	Enhancers	HMEC	breast
43	chr12:48109000-48110400	Enhancers	Esophagus	oesophagus
44	chr12:48109000-48110400	Enhancers	Psoas Muscle	Psoas
45	chr12:48109000-48112200	Enhancers	Primary T cells fromperipheralblood	blood
46	chr12:48109000-48112200	Enhancers	Fetal Thymus	thymus
47	chr12:48109000-48112400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:48109000-48112400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:48109000-48112600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:48109000-48112600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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