Variant report

Variant	rs1991440
Chromosome Location	chr3:134092993-134092994
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	MAX	chr3:134092873-134094398	HCT-116	colon:	n/a	chr3:134093443-134093453
2	POLR2A	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
3	MAX	chr3:134092316-134093921	H1-hESC	embryonic stem cell:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
4	NR2F2	chr3:134092953-134094330	MCF-7	breast:	n/a	n/a
5	TEAD4	chr3:134092966-134094186	A549	lung:	n/a	n/a
6	ZBTB33	chr3:134092971-134093556	SK-N-SH	brain:	n/a	chr3:134093143-134093153
7	TAF7	chr3:134091817-134093873	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F4	chr3:134092984-134093601	MCF10A-Er-Src	breast:	n/a	chr3:134093439-134093451
9	POLR2A	chr3:134092946-134093686	U87	brain:	n/a	n/a
10	HDAC2	chr3:134092846-134094356	MCF-7	breast:	n/a	n/a
11	MYBL2	chr3:134092963-134093605	HepG2	liver:	n/a	n/a
12	EP300	chr3:134091790-134094514	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134091915-134091931 chr3:134092363-134092379 chr3:134092748-134092757
13	POLR2A	chr3:134086772-134094312	ECC-1	luminal epithelium:	n/a	n/a
14	RCOR1	chr3:134091947-134094409	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:134091825-134094472	Hela-S3	cervix:	n/a	n/a
16	EP300	chr3:134092297-134094402	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134092363-134092379 chr3:134092748-134092757
17	SRF	chr3:134092989-134093722	ECC-1	luminal epithelium:	n/a	chr3:134093505-134093515
18	RFX5	chr3:134091836-134094520	Hela-S3	cervix:	n/a	n/a
19	E2F1	chr3:134092992-134094287	Hela-S3	cervix:	n/a	chr3:134093439-134093451 chr3:134093293-134093304
20	JUND	chr3:134092195-134093605	H1-hESC	embryonic stem cell:	n/a	chr3:134092661-134092670
21	PML	chr3:134092889-134093677	MCF-7	breast:	n/a	n/a
22	FOXM1	chr3:134092927-134094306	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:134091789-134093988	HUVEC	blood vessel:	n/a	n/a
24	TEAD4	chr3:134091947-134094381	ECC-1	luminal epithelium:	n/a	n/a
25	MAZ	chr3:134092048-134093871	HepG2	liver:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
26	TCF12	chr3:134091783-134094382	ECC-1	luminal epithelium:	n/a	chr3:134092197-134092205 chr3:134093938-134093947 chr3:134091915-134091925
27	TAF1	chr3:134092394-134093652	SK-N-SH	brain:	n/a	n/a
28	CEBPB	chr3:134092476-134094394	Hela-S3	cervix:	n/a	n/a
29	NFIC	chr3:134092968-134093550	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:134090064-134093861	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr3:134092182-134093742	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:134092950-134093797	Gliobla	brain:	n/a	n/a
33	MAX	chr3:134092923-134094094	SK-N-SH	brain:	n/a	chr3:134093443-134093453
34	ETS1	chr3:134092993-134093376	A549	lung:	n/a	n/a
35	BCL3	chr3:134092965-134094139	A549	lung:	n/a	chr3:134093526-134093535 chr3:134093979-134093988 chr3:134093483-134093496
36	POLR2A	chr3:134090674-134093906	H1-hESC	embryonic stem cell:	n/a	n/a
37	TEAD4	chr3:134092988-134093698	HCT-116	colon:	n/a	n/a
38	CTCF	chr3:134092960-134093110	SAEC	small airway:	n/a	n/a
39	TAF1	chr3:134091772-134094474	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr3:134092985-134094231	A549	lung:	n/a	chr3:134093458-134093467
41	MAX	chr3:134092902-134094182	HepG2	liver:	n/a	chr3:134093443-134093453
42	GTF2F1	chr3:134092122-134093629	H1-hESC	embryonic stem cell:	n/a	chr3:134092292-134092303
43	POLR2A	chr3:134092363-134093617	MCF-7	breast:	n/a	n/a
44	REST	chr3:134092944-134093525	MCF-7	breast:	n/a	chr3:134093018-134093031 chr3:134093487-134093500 chr3:134092989-134093002
45	JUND	chr3:134092329-134093683	SK-N-SH	brain:	n/a	chr3:134092661-134092670
46	BHLHE40	chr3:134092920-134094245	HepG2	liver:	n/a	chr3:134093485-134093501
47	CTCF	chr3:134092960-134093110	SK-N-SH_RA	brain:	n/a	n/a
48	TCF12	chr3:134092937-134093533	A549	lung:	n/a	n/a
49	TCF7L2	chr3:134092974-134094381	HEK293	kidney:	n/a	chr3:134093922-134093929 chr3:134093379-134093393
50	JUND	chr3:134092299-134093877	SK-N-SH	brain:	n/a	chr3:134092661-134092670

No.	Distal block	Cell Line	Cell type
1	chr3:134091805..134100491-chr3:134198620..134206897,15	MCF-7	breast:
2	chr3:134092139..134093139-chr9:91933170..91933720,2	Hela-S3	cervix:
3	chr3:134089711..134094738-chr3:134202793..134208651,12	MCF-7	breast:
4	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:

Variant related genes	Relation type
AMOTL2	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11919447	0.89[EUR][1000 genomes]
rs11923513	0.89[EUR][1000 genomes]
rs17312996	0.89[EUR][1000 genomes]
rs17313003	0.87[EUR][1000 genomes]
rs6784751	0.89[EUR][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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134090400-134094400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:134090600-134093600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:134091000-134094000	Active TSS	Fetal Kidney	kidney
4	chr3:134091200-134093600	Active TSS	Esophagus	oesophagus
5	chr3:134091200-134093600	Active TSS	HSMMtube	muscle
6	chr3:134091200-134093800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:134091200-134093800	Active TSS	Aorta	Aorta
8	chr3:134091200-134094000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:134091200-134094000	Active TSS	Lung	lung
10	chr3:134091400-134093400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:134091400-134093600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:134091400-134093600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:134091400-134093600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:134091400-134093600	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr3:134091400-134093800	Active TSS	Placenta Amnion	Placenta Amnion
16	chr3:134091400-134094000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr3:134091400-134094000	Active TSS	Colon Smooth Muscle	Colon
18	chr3:134091400-134094000	Active TSS	NHDF-Ad	bronchial
19	chr3:134091400-134094200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:134091400-134094400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr3:134091600-134093000	Active TSS	Duodenum Mucosa	Duodenum
22	chr3:134091600-134093400	Active TSS	HMEC	breast
23	chr3:134091600-134093600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:134091600-134093600	Active TSS	Adipose Nuclei	Adipose
25	chr3:134091600-134093600	Active TSS	Brain Cingulate Gyrus	brain
26	chr3:134091600-134093600	Active TSS	Brain Hippocampus Middle	brain
27	chr3:134091600-134093600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr3:134091600-134093600	Active TSS	Fetal Brain Male	brain
29	chr3:134091600-134093600	Active TSS	Fetal Brain Female	brain
30	chr3:134091600-134093600	Active TSS	Fetal Heart	heart
31	chr3:134091600-134093600	Active TSS	Fetal Muscle Trunk	muscle
32	chr3:134091600-134093600	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:134091600-134093600	Active TSS	Right Atrium	heart
34	chr3:134091600-134093600	Active TSS	HSMM	muscle
35	chr3:134091600-134093600	Active TSS	HUVEC	blood vessel
36	chr3:134091600-134093600	Active TSS	NH-A	brain
37	chr3:134091600-134093800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:134091600-134093800	Active TSS	Brain Angular Gyrus	brain
39	chr3:134091600-134093800	Active TSS	Fetal Intestine Large	intestine
40	chr3:134091600-134094000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:134091600-134094000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr3:134091600-134094000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:134091600-134094000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr3:134091600-134094000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:134091600-134094000	Active TSS	Brain Substantia Nigra	brain
46	chr3:134091600-134094000	Active TSS	Gastric	stomach
47	chr3:134091600-134094000	Active TSS	Right Ventricle	heart
48	chr3:134091600-134094200	Active TSS	Left Ventricle	heart
49	chr3:134091600-134094400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:134091800-134093200	Bivalent/Poised TSS	Thymus	Thymus

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