Variant report

Variant	rs12477748
Chromosome Location	chr2:10148704-10148705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:10148640-10148790	HVMF	connective:	n/a	n/a
2	CTCF	chr2:10148640-10148790	K562	blood:	n/a	n/a
3	CTCF	chr2:10148660-10148810	HMF	breast:	n/a	n/a
4	RCOR1	chr2:10148675-10148866	K562	blood:	n/a	n/a
5	MAX	chr2:10148368-10148832	K562	blood:	n/a	n/a
6	CTCF	chr2:10148690-10148855	K562	blood:	n/a	n/a
7	NR2F2	chr2:10148607-10148896	K562	blood:	n/a	n/a
8	CTCF	chr2:10148700-10148850	WERI-Rb-1	eye:	n/a	n/a
9	CTCF	chr2:10148660-10148810	AG10803	skin:	n/a	n/a
10	CTCF	chr2:10148627-10149048	K562	blood:	n/a	n/a
11	CTCF	chr2:10148660-10148810	AG04449	skin:	n/a	n/a
12	SMC3	chr2:10148659-10148864	K562	blood:	n/a	n/a
13	CTCF	chr2:10148680-10148830	AG10803	skin:	n/a	n/a
14	CTCF	chr2:10148660-10148810	HVMF	connective:	n/a	n/a
15	ZNF143	chr2:10148688-10148775	K562	blood:	n/a	n/a
16	CTCF	chr2:10148611-10148942	K562	blood:	n/a	n/a
17	CTCF	chr2:10148668-10148856	Medullo	brain:	n/a	n/a
18	CTCF	chr2:10148608-10148857	K562	blood:	n/a	n/a
19	RAD21	chr2:10148657-10148833	K562	blood:	n/a	n/a
20	CTCF	chr2:10148628-10148912	K562	blood:	n/a	n/a
21	E2F6	chr2:10148689-10148882	K562	blood:	n/a	n/a
22	CTCF	chr2:10148680-10148830	AG04449	skin:	n/a	n/a
23	CTCF	chr2:10148680-10148830	HRPEpiC	eye:	n/a	n/a
24	CTCF	chr2:10148680-10148830	HCFaa	heart:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10146994..10149729-chr2:10182824..10184485,2	MCF-7	breast:
2	chr2:10148500..10150133-chr2:10169876..10172659,2	K562	blood:
3	chr2:10147171..10148722-chr2:10150073..10151791,3	K562	blood:
4	chr2:10147491..10150465-chr2:10152525..10155691,3	MCF-7	breast:
5	chr2:10143972..10145495-chr2:10148319..10150993,2	K562	blood:
6	chr2:10147901..10149984-chr2:10215589..10217531,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188525	TF binding region
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12470881	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12992130	0.89[AFR][1000 genomes]
rs34521538	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4669517	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
2	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
3	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:10137600-10149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:10139800-10150400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:10141600-10160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:10145800-10151000	Enhancers	Pancreas	Pancrea
10	chr2:10146400-10148800	Enhancers	Liver	Liver
11	chr2:10146400-10148800	Enhancers	Gastric	stomach
12	chr2:10146400-10150800	Enhancers	Colon Smooth Muscle	Colon
13	chr2:10146400-10150800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr2:10146400-10151200	Enhancers	Placenta	Placenta
15	chr2:10146600-10148800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:10146600-10148800	Enhancers	Right Atrium	heart
17	chr2:10146800-10148800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:10146800-10150200	Enhancers	Rectal Smooth Muscle	rectum
19	chr2:10146800-10150800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:10146800-10150800	Enhancers	HSMM	muscle
21	chr2:10146800-10151000	Enhancers	NHDF-Ad	bronchial
22	chr2:10146800-10151200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:10147000-10148800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:10147000-10150600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:10147000-10150800	Enhancers	HSMMtube	muscle
26	chr2:10147200-10149000	Weak transcription	Small Intestine	intestine
27	chr2:10147200-10149400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:10147200-10149400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:10147200-10149800	Enhancers	Stomach Smooth Muscle	stomach
30	chr2:10147200-10150600	Weak transcription	Esophagus	oesophagus
31	chr2:10147200-10150800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:10147200-10151200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:10147400-10149400	Weak transcription	Stomach Mucosa	stomach
34	chr2:10147400-10149800	Weak transcription	Fetal Heart	heart
35	chr2:10147600-10151000	Enhancers	NHLF	lung
36	chr2:10147800-10151200	Enhancers	Fetal Muscle Leg	muscle
37	chr2:10148000-10148800	Enhancers	Left Ventricle	heart
38	chr2:10148000-10149200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:10148000-10149800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:10148200-10148800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
41	chr2:10148200-10148800	Enhancers	K562	blood
42	chr2:10148200-10151000	Enhancers	Ovary	ovary
43	chr2:10148200-10151800	Enhancers	Lung	lung
44	chr2:10148400-10148800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:10148400-10149000	Bivalent Enhancer	HepG2	liver
46	chr2:10148400-10150200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:10148400-10151200	Enhancers	Right Ventricle	heart
48	chr2:10148600-10148800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:10148600-10148800	Enhancers	Adipose Nuclei	Adipose
50	chr2:10148600-10148800	Enhancers	Colonic Mucosa	Colon

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