Variant report

Variant	rs12113645
Chromosome Location	chr7:3342608-3342609
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	POLR2A	chr7:3342598-3342625	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF7L2	chr7:3342190-3343032	HEK293	kidney:	n/a	n/a
3	RAD21	chr7:3341429-3344236	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236708	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10276122	1.00[AMR][1000 genomes]
rs28867718	1.00[AMR][1000 genomes]
rs56753309	1.00[AMR][1000 genomes]
rs57348351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57447860	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57456054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57941647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58262427	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58317645	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58502351	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58843670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58949619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58993463	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59064718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59223438	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60666675	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61007926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73284319	1.00[AMR][1000 genomes]
rs73284328	1.00[EUR][1000 genomes]
rs73286317	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286326	1.00[AFR][1000 genomes]
rs73286330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73286364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73288369	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73290049	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73290052	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73290058	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73290066	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73292162	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73292182	1.00[EUR][1000 genomes]
rs73292183	1.00[EUR][1000 genomes]
rs73292190	1.00[EUR][1000 genomes]
rs73294209	1.00[EUR][1000 genomes]
rs73297033	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3340000-3343400	Active TSS	Aorta	Aorta
2	chr7:3340200-3342800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:3340200-3343000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr7:3340200-3343200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:3340400-3342800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr7:3340400-3343000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:3341400-3342800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr7:3341400-3342800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr7:3341600-3342800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr7:3341600-3342800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
11	chr7:3341600-3342800	Bivalent/Poised TSS	NHDF-Ad	bronchial
12	chr7:3342200-3342800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:3342200-3342800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:3342200-3343200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:3342200-3344600	Weak transcription	Psoas Muscle	Psoas
16	chr7:3342400-3343800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:3342400-3344000	Weak transcription	Pancreas	Pancrea
18	chr7:3342600-3342800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr7:3342600-3342800	Active TSS	Adipose Nuclei	Adipose
20	chr7:3342600-3342800	Active TSS	Fetal Brain Female	brain
21	chr7:3342600-3342800	Enhancers	Fetal Lung	lung
22	chr7:3342600-3342800	Active TSS	Stomach Smooth Muscle	stomach
23	chr7:3342600-3343000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr7:3342600-3343000	Enhancers	Fetal Heart	heart
25	chr7:3342600-3343000	Enhancers	Rectal Smooth Muscle	rectum
26	chr7:3342600-3343400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:3342600-3343600	Weak transcription	HepG2	liver
28	chr7:3342600-3344200	Enhancers	Colon Smooth Muscle	Colon
29	chr7:3342600-3344600	Weak transcription	Fetal Brain Male	brain
30	chr7:3342600-3347200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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