Variant report

Variant	rs4682481
Chromosome Location	chr3:112983855-112983856
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	chr3:112983691-112984491	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr3:112983009-112984710	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr3:112983556-112984650	ECC-1	luminal epithelium:	n/a	chr3:112984207-112984221
4	ESR1	chr3:112983641-112984684	ECC-1	luminal epithelium:	n/a	n/a
5	ESR1	chr3:112983616-112984023	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr3:112982914-112984707	ECC-1	luminal epithelium:	n/a	chr3:112984207-112984221
7	SIN3A	chr3:112983048-112983890	H1-hESC	embryonic stem cell:	n/a	chr3:112983788-112983802
8	TEAD4	chr3:112983625-112984624	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr3:112983589-112984650	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr3:112983533-112984651	ECC-1	luminal epithelium:	n/a	n/a
11	FOXM1	chr3:112983697-112984737	ECC-1	luminal epithelium:	n/a	n/a
12	TCF12	chr3:112982915-112984776	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr3:112983634-112984564	ECC-1	luminal epithelium:	n/a	n/a
14	NR3C1	chr3:112983665-112984607	ECC-1	luminal epithelium:	n/a	chr3:112984457-112984483 chr3:112983834-112983841 chr3:112984461-112984479
15	TEAD4	chr3:112983617-112984587	ECC-1	luminal epithelium:	n/a	n/a
16	ESR1	chr3:112983517-112984713	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10511323	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710894	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11717833	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11919134	0.81[AMR][1000 genomes]
rs11928342	0.82[JPT][hapmap];0.92[AMR][1000 genomes]
rs12485329	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492273	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494864	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631733	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12638030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16860758	0.93[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16860787	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1875111	0.81[JPT][hapmap]
rs2036282	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2201971	0.80[AMR][1000 genomes]
rs2270781	0.83[JPT][hapmap]
rs34284771	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3814398	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs3846046	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3856718	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3856719	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3856720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682131	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682132	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682478	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682479	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682480	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4682483	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73235136	0.81[ASN][1000 genomes]
rs73235142	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235143	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235147	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235153	0.83[ASN][1000 genomes]
rs7641410	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs775222	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
9	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:112976400-112988600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:112978800-112984400	Genic enhancers	Stomach Smooth Muscle	stomach
13	chr3:112979400-112984800	Genic enhancers	Fetal Stomach	stomach
14	chr3:112979600-112985600	Enhancers	Fetal Brain Female	brain
15	chr3:112980600-112984000	Enhancers	HSMMtube	muscle
16	chr3:112980600-112984400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:112981000-112984200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:112981000-112984200	Enhancers	HSMM	muscle
19	chr3:112981000-112986600	Enhancers	Brain Substantia Nigra	brain
20	chr3:112981200-112984200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:112981200-112991000	Genic enhancers	Fetal Muscle Leg	muscle
22	chr3:112981400-112984200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:112981400-112984400	Enhancers	Brain Anterior Caudate	brain
24	chr3:112981400-112984800	Enhancers	Fetal Thymus	thymus
25	chr3:112981400-112987200	Weak transcription	Aorta	Aorta
26	chr3:112981400-112989800	Weak transcription	Gastric	stomach
27	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:112981800-112984200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:112981800-112984800	Enhancers	Psoas Muscle	Psoas
30	chr3:112981800-112985400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr3:112982000-112984000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:112982000-112984800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr3:112982000-112984800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:112982000-112985000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:112982000-112985600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:112982000-112985800	Weak transcription	Esophagus	oesophagus
37	chr3:112982000-112986200	Weak transcription	Ovary	ovary
38	chr3:112982000-112989800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:112982200-112984200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:112982200-112984800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:112982200-112986000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:112982200-112987200	Weak transcription	Fetal Intestine Large	intestine
43	chr3:112982200-112988800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:112982200-112989400	Weak transcription	Adipose Nuclei	Adipose
45	chr3:112982400-112984600	Enhancers	Brain Germinal Matrix	brain
46	chr3:112982400-112985000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:112982400-112985000	Enhancers	Brain Hippocampus Middle	brain
48	chr3:112982600-112984800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr3:112982600-112989000	Weak transcription	NHEK	skin
50	chr3:112982800-112984600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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