Variant report

Variant	rs7629849
Chromosome Location	chr3:134092398-134092399
allele	G/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	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
2	MAX	chr3:134092316-134093921	H1-hESC	embryonic stem cell:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
3	SP4	chr3:134092115-134092819	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP4	chr3:134092016-134092681	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF7	chr3:134091817-134093873	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr3:134091790-134094514	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134091915-134091931 chr3:134092363-134092379 chr3:134092748-134092757
7	POLR2A	chr3:134086772-134094312	ECC-1	luminal epithelium:	n/a	n/a
8	RCOR1	chr3:134091947-134094409	Hela-S3	cervix:	n/a	n/a
9	GTF2F1	chr3:134092177-134092802	Hela-S3	cervix:	n/a	chr3:134092292-134092303
10	POLR2A	chr3:134091825-134094472	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:134092329-134092894	U87	brain:	n/a	n/a
12	EP300	chr3:134092297-134094402	ECC-1	luminal epithelium:	n/a	chr3:134093458-134093467 chr3:134092363-134092379 chr3:134092748-134092757
13	RFX5	chr3:134091836-134094520	Hela-S3	cervix:	n/a	n/a
14	GATA3	chr3:134092380-134092957	SK-N-SH	brain:	n/a	n/a
15	JUND	chr3:134092195-134093605	H1-hESC	embryonic stem cell:	n/a	chr3:134092661-134092670
16	SP1	chr3:134092003-134092800	A549	lung:	n/a	n/a
17	POLR2A	chr3:134092263-134092712	A549	lung:	n/a	n/a
18	RAD21	chr3:134092107-134092913	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:134091789-134093988	HUVEC	blood vessel:	n/a	n/a
20	SIN3AK20	chr3:134091772-134092923	SK-N-SH	brain:	n/a	n/a
21	TEAD4	chr3:134091947-134094381	ECC-1	luminal epithelium:	n/a	n/a
22	MAZ	chr3:134092048-134093871	HepG2	liver:	n/a	chr3:134092343-134092353 chr3:134093443-134093453
23	TCF12	chr3:134091783-134094382	ECC-1	luminal epithelium:	n/a	chr3:134092197-134092205 chr3:134093938-134093947 chr3:134091915-134091925
24	FOSL2	chr3:134092376-134092910	SK-N-SH	brain:	n/a	chr3:134092661-134092670
25	TAF1	chr3:134092394-134093652	SK-N-SH	brain:	n/a	n/a
26	MAX	chr3:134092346-134092863	ECC-1	luminal epithelium:	n/a	n/a
27	MXI1	chr3:134092032-134092827	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:134090064-134093861	SK-N-SH	brain:	n/a	n/a
29	USF2	chr3:134091903-134092715	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:134092182-134093742	MCF10A-Er-Src	breast:	n/a	n/a
31	CTCF	chr3:134092280-134092430	HCPEpiC	choroid plexus:	n/a	chr3:134092340-134092353
32	E2F4	chr3:134092312-134092750	MCF10A-Er-Src	breast:	n/a	chr3:134092662-134092671 chr3:134092660-134092669 chr3:134092338-134092347
33	GATA2	chr3:134091958-134092513	SH-SY5Y	brain:	n/a	chr3:134092098-134092107
34	JUND	chr3:134092363-134092871	T-47D	breast:	n/a	chr3:134092661-134092670
35	SIN3AK20	chr3:134092007-134092839	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:134090674-134093906	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:134079921-134092871	ECC-1	luminal epithelium:	n/a	n/a
38	TAF1	chr3:134091772-134094474	H1-hESC	embryonic stem cell:	n/a	n/a
39	REST	chr3:134092392-134092846	A549	lung:	n/a	n/a
40	GTF2F1	chr3:134092122-134093629	H1-hESC	embryonic stem cell:	n/a	chr3:134092292-134092303
41	POLR2A	chr3:134092363-134093617	MCF-7	breast:	n/a	n/a
42	JUND	chr3:134092329-134093683	SK-N-SH	brain:	n/a	chr3:134092661-134092670
43	JUND	chr3:134092299-134093877	SK-N-SH	brain:	n/a	chr3:134092661-134092670
44	SMC3	chr3:134091260-134094465	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr3:134092317-134093676	ECC-1	luminal epithelium:	n/a	n/a
46	BRCA1	chr3:134092282-134094562	Hela-S3	cervix:	n/a	n/a
47	ATF2	chr3:134091851-134093550	H1-hESC	embryonic stem cell:	n/a	chr3:134092660-134092671 chr3:134092658-134092672
48	EP300	chr3:134092318-134092897	A549	lung:	n/a	chr3:134092363-134092379 chr3:134092748-134092757
49	NFIC	chr3:134092260-134094344	SK-N-SH	brain:	n/a	n/a
50	JUND	chr3:134091923-134094010	H1-hESC	embryonic stem cell:	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:
5	chr13:73301301..73302072-chr3:134091793..134092639,2	Hela-S3	cervix:

Variant related genes	Relation type
AMOTL2	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000136122	Chromatin interaction
ENSG00000204899	Chromatin interaction
ENSG00000182923	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11925583	1.00[EUR][1000 genomes]
rs2173448	1.00[EUR][1000 genomes]
rs2400272	1.00[EUR][1000 genomes]
rs35161002	1.00[EUR][1000 genomes]
rs56874024	1.00[EUR][1000 genomes]
rs59473547	1.00[EUR][1000 genomes]
rs60048996	1.00[EUR][1000 genomes]
rs6798709	1.00[EUR][1000 genomes]
rs7433301	1.00[EUR][1000 genomes]
rs7623024	1.00[EUR][1000 genomes]
rs7643419	1.00[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134082200-134092800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:134087200-134092600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:134087600-134092400	Transcr. at gene 5' and 3'	A549	lung
4	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Osteobl	bone
6	chr3:134088200-134092600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:134088400-134092600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134088600-134092400	Transcr. at gene 5' and 3'	NHLF	lung
9	chr3:134089200-134092600	Transcr. at gene 5' and 3'	NHEK	skin
10	chr3:134089400-134092400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
11	chr3:134090400-134094400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr3:134090600-134092600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
13	chr3:134090600-134093600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:134091000-134092400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:134091000-134094000	Active TSS	Fetal Kidney	kidney
16	chr3:134091200-134092400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:134091200-134093600	Active TSS	Esophagus	oesophagus
18	chr3:134091200-134093600	Active TSS	HSMMtube	muscle
19	chr3:134091200-134093800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:134091200-134093800	Active TSS	Aorta	Aorta
21	chr3:134091200-134094000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:134091200-134094000	Active TSS	Lung	lung
23	chr3:134091400-134092600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:134091400-134092600	Flanking Active TSS	Liver	Liver
25	chr3:134091400-134092800	Active TSS	Spleen	Spleen
26	chr3:134091400-134093400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:134091400-134093600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:134091400-134093600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:134091400-134093600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:134091400-134093600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr3:134091400-134093800	Active TSS	Placenta Amnion	Placenta Amnion
32	chr3:134091400-134094000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr3:134091400-134094000	Active TSS	Colon Smooth Muscle	Colon
34	chr3:134091400-134094000	Active TSS	NHDF-Ad	bronchial
35	chr3:134091400-134094200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:134091400-134094400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr3:134091600-134092400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:134091600-134093000	Active TSS	Duodenum Mucosa	Duodenum
39	chr3:134091600-134093400	Active TSS	HMEC	breast
40	chr3:134091600-134093600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:134091600-134093600	Active TSS	Adipose Nuclei	Adipose
42	chr3:134091600-134093600	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:134091600-134093600	Active TSS	Brain Hippocampus Middle	brain
44	chr3:134091600-134093600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:134091600-134093600	Active TSS	Fetal Brain Male	brain
46	chr3:134091600-134093600	Active TSS	Fetal Brain Female	brain
47	chr3:134091600-134093600	Active TSS	Fetal Heart	heart
48	chr3:134091600-134093600	Active TSS	Fetal Muscle Trunk	muscle
49	chr3:134091600-134093600	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:134091600-134093600	Active TSS	Right Atrium	heart

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