Variant report

Variant	rs73346100
Chromosome Location	chr12:58008248-58008249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:58008049-58008390	K562	blood:	n/a	n/a
2	SP2	chr12:58007932-58008251	H1-hESC	embryonic stem cell:	n/a	chr12:58008202-58008217
3	USF1	chr12:58008065-58008303	A549	lung:	n/a	n/a
4	USF1	chr12:58008024-58008335	GM12878	blood:	n/a	n/a
5	MAX	chr12:58008061-58008302	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF2	chr12:58007987-58008734	GM12878	blood:	n/a	n/a
7	BHLHE40	chr12:58008076-58008730	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:58008248-58008368	GM12878	blood:	n/a	n/a
9	MTA3	chr12:58007941-58008759	GM12878	blood:	n/a	n/a
10	MAX	chr12:58008045-58008848	NB4	blood:	n/a	chr12:58008824-58008839 chr12:58008828-58008838
11	NFYA	chr12:58007922-58008349	K562	blood:	n/a	chr12:58008145-58008163
12	RFX5	chr12:58007989-58008316	GM12878	blood:	n/a	n/a
13	SP1	chr12:58007922-58008394	GM12878	blood:	n/a	n/a
14	ZNF143	chr12:58008145-58008593	GM12878	blood:	n/a	n/a
15	RUNX3	chr12:58008161-58008716	GM12878	blood:	n/a	n/a
16	PAX5	chr12:58008199-58008752	GM12878	blood:	n/a	n/a
17	NFYA	chr12:58007969-58008250	Hela-S3	cervix:	n/a	chr12:58008145-58008163
18	USF1	chr12:58008027-58008353	A549	lung:	n/a	n/a
19	CEBPB	chr12:58007908-58008266	K562	blood:	n/a	chr12:58008067-58008078
20	USF2	chr12:58008038-58008356	K562	blood:	n/a	n/a
21	PBX3	chr12:58007935-58008306	SK-N-SH	brain:	n/a	n/a
22	USF1	chr12:58008019-58008367	HCT-116	colon:	n/a	n/a
23	USF1	chr12:58007942-58008353	A549	lung:	n/a	n/a
24	CHD2	chr12:58007810-58008338	K562	blood:	n/a	n/a
25	MAZ	chr12:58008020-58008303	K562	blood:	n/a	n/a
26	CHD2	chr12:58008026-58008291	H1-hESC	embryonic stem cell:	n/a	n/a
27	RUNX3	chr12:58008111-58008491	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:58007680-58008321	SK-N-MC	brain:	n/a	n/a
29	MAZ	chr12:58008050-58008610	GM12878	blood:	n/a	n/a
30	PBX3	chr12:58008078-58008266	GM12878	blood:	n/a	n/a
31	USF1	chr12:58008000-58008335	SK-N-SH	brain:	n/a	n/a
32	USF1	chr12:58007910-58008418	K562	blood:	n/a	n/a
33	USF2	chr12:58008004-58008335	H1-hESC	embryonic stem cell:	n/a	n/a
34	ATF3	chr12:58008014-58008314	K562	blood:	n/a	n/a
35	POLR2A	chr12:58007845-58008469	Raji	blood:	n/a	n/a
36	CREB1	chr12:58007983-58008272	A549	lung:	n/a	n/a
37	SP2	chr12:58007997-58008351	K562	blood:	n/a	chr12:58008202-58008217
38	USF1	chr12:58007913-58008373	ECC-1	luminal epithelium:	n/a	n/a
39	NFYB	chr12:58007860-58008551	K562	blood:	n/a	chr12:58008151-58008166
40	USF1	chr12:58007954-58008357	A549	lung:	n/a	n/a
41	USF1	chr12:58008040-58008255	HepG2	liver:	n/a	n/a
42	USF1	chr12:58008047-58008303	GM12878	blood:	n/a	n/a
43	MAX	chr12:58007995-58008343	K562	blood:	n/a	n/a
44	NFYB	chr12:58007957-58008362	GM12878	blood:	n/a	chr12:58008151-58008166
45	TBL1XR1	chr12:58008074-58008274	K562	blood:	n/a	n/a
46	USF1	chr12:58008021-58008337	SK-N-SH_RA	brain:	n/a	n/a
47	IRF1	chr12:58008017-58008325	K562	blood:	n/a	n/a
48	USF1	chr12:58007954-58008434	HCT-116	colon:	n/a	n/a
49	TBP	chr12:58007898-58008248	K562	blood:	n/a	n/a
50	USF2	chr12:58008009-58008290	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57911754..57916322-chr12:58006406..58010716,5	K562	blood:
2	chr12:57854178..57856393-chr12:58005789..58008256,3	K562	blood:
3	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
4	chr12:57892478..57894740-chr12:58006142..58008775,2	MCF-7	breast:
5	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
6	chr12:58004396..58008788-chr12:58163385..58167140,4	MCF-7	breast:
7	chr12:58007718..58010411-chr12:58087376..58090012,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARHGEF25	TF binding region
ENSG00000208028	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000135506	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11172270	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12578587	1.00[EUR][1000 genomes]
rs28620262	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7294447	1.00[EUR][1000 genomes]
rs7960103	1.00[EUR][1000 genomes]
rs7966948	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58011400	Weak transcription	Lung	lung
2	chr12:58005600-58013200	Weak transcription	Gastric	stomach
3	chr12:58005800-58008400	Weak transcription	Aorta	Aorta
4	chr12:58006000-58010000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
5	chr12:58006200-58008600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr12:58006200-58010000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:58006200-58010200	Weak transcription	NHDF-Ad	bronchial
8	chr12:58006200-58010400	Weak transcription	NH-A	brain
9	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:58006400-58008400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:58006400-58008600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:58006400-58009000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:58006400-58009000	Weak transcription	Brain Anterior Caudate	brain
14	chr12:58006400-58009000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:58006400-58009400	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:58006400-58011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:58006600-58009400	Weak transcription	NHLF	lung
18	chr12:58006600-58010000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:58006600-58011000	Strong transcription	Fetal Lung	lung
20	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
21	chr12:58006800-58008400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:58006800-58008600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
23	chr12:58006800-58009200	Genic enhancers	Colon Smooth Muscle	Colon
24	chr12:58006800-58010200	Weak transcription	Fetal Brain Male	brain
25	chr12:58006800-58011400	Strong transcription	Ovary	ovary
26	chr12:58006800-58011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:58006800-58011600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:58006800-58011600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:58006800-58011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:58006800-58012000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:58007000-58008600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:58007000-58009200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
33	chr12:58007000-58009600	Genic enhancers	Fetal Muscle Leg	muscle
34	chr12:58007000-58012000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:58007200-58008600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:58007200-58008600	Enhancers	Spleen	Spleen
37	chr12:58007200-58009400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:58007200-58009800	Strong transcription	Osteobl	bone
39	chr12:58007200-58011200	Strong transcription	Fetal Brain Female	brain
40	chr12:58007400-58009000	Enhancers	GM12878-XiMat	blood
41	chr12:58007400-58009400	Enhancers	Primary B cells from cord blood	blood
42	chr12:58007400-58009600	Genic enhancers	Left Ventricle	heart
43	chr12:58007400-58010200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:58007600-58008400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:58007600-58008400	Flanking Active TSS	K562	blood
46	chr12:58007600-58009200	Bivalent Enhancer	Fetal Thymus	thymus
47	chr12:58007600-58010000	Weak transcription	Esophagus	oesophagus
48	chr12:58007600-58010600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:58007800-58008400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr12:58007800-58008400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin

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