Variant report

Variant	rs536488989
Chromosome Location	chr3:134070259-134070260
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	TEAD4	chr3:134069580-134070283	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr3:134069556-134070320	ECC-1	luminal epithelium:	n/a	chr3:134070094-134070111
3	ESR1	chr3:134069763-134070326	T-47D	breast:	n/a	n/a
4	HDAC2	chr3:134069707-134070357	MCF-7	breast:	n/a	chr3:134070195-134070204
5	TCF7L2	chr3:134069788-134070344	MCF-7	breast:	n/a	chr3:134070042-134070056
6	NFIC	chr3:134069578-134070506	ECC-1	luminal epithelium:	n/a	chr3:134070094-134070111
7	RAD21	chr3:134069674-134070382	MCF-7	breast:	n/a	n/a
8	SP1	chr3:134069500-134070311	HCT-116	colon:	n/a	chr3:134069739-134069753 chr3:134070106-134070120
9	NR2F2	chr3:134069662-134070462	MCF-7	breast:	n/a	n/a
10	ZNF217	chr3:134069744-134070400	MCF-7	breast:	n/a	n/a
11	TCF12	chr3:134069386-134070624	MCF-7	breast:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
12	MAX	chr3:134069551-134070304	HCT-116	colon:	n/a	chr3:134069852-134069861
13	ELF1	chr3:134069177-134070324	MCF-7	breast:	n/a	n/a
14	MAX	chr3:134069617-134070317	ECC-1	luminal epithelium:	n/a	chr3:134069852-134069861
15	MAX	chr3:134069542-134070379	HCT-116	colon:	n/a	chr3:134069852-134069861
16	JUND	chr3:134069592-134070358	MCF-7	breast:	n/a	n/a
17	TCF12	chr3:134069540-134070380	ECC-1	luminal epithelium:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
18	SIN3AK20	chr3:134069593-134070439	MCF-7	breast:	n/a	n/a
19	MAX	chr3:134069228-134070274	MCF-7	breast:	n/a	chr3:134069852-134069861
20	FOXA1	chr3:134069750-134070314	T-47D	breast:	n/a	n/a
21	TCF12	chr3:134069464-134070399	ECC-1	luminal epithelium:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
22	GATA3	chr3:134069707-134070342	T-47D	breast:	n/a	n/a
23	JUND	chr3:134069590-134070320	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:134070224-134070559	ECC-1	luminal epithelium:	n/a	n/a
25	EP300	chr3:134069652-134070263	T-47D	breast:	n/a	chr3:134070194-134070204
26	ELF1	chr3:134069576-134070459	MCF-7	breast:	n/a	n/a
27	EP300	chr3:134069604-134070435	MCF-7	breast:	n/a	chr3:134070194-134070204 chr3:134070406-134070420
28	MAX	chr3:134069576-134070432	MCF-7	breast:	n/a	chr3:134069852-134069861
29	FOXA1	chr3:134069769-134070376	T-47D	breast:	n/a	n/a
30	ESR1	chr3:134069876-134070369	T-47D	breast:	n/a	n/a
31	GATA3	chr3:134069560-134070443	MCF-7	breast:	n/a	chr3:134069698-134069707
32	FOXM1	chr3:134069639-134070455	MCF-7	breast:	n/a	n/a
33	NR2F2	chr3:134069592-134070510	MCF-7	breast:	n/a	n/a
34	CHD2	chr3:134069979-134070347	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:134069255-134074808	A549	lung:	n/a	n/a
36	GATA3	chr3:134069709-134070360	MCF-7	breast:	n/a	n/a
37	TCF12	chr3:134069559-134070425	MCF-7	breast:	n/a	chr3:134069806-134069813 chr3:134069732-134069742 chr3:134070314-134070324
38	EP300	chr3:134069587-134070374	T-47D	breast:	n/a	chr3:134070194-134070204
39	HDAC2	chr3:134069615-134070400	MCF-7	breast:	n/a	chr3:134070195-134070204
40	GATA3	chr3:134069445-134070537	MCF-7	breast:	n/a	chr3:134069698-134069707
41	POLR2A	chr3:134070006-134070334	MCF10A-Er-Src	breast:	n/a	n/a
42	SIN3AK20	chr3:134069391-134070562	MCF-7	breast:	n/a	n/a
43	TEAD4	chr3:134069628-134070264	MCF-7	breast:	n/a	n/a
44	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
45	EP300	chr3:134069506-134070423	ECC-1	luminal epithelium:	n/a	chr3:134070194-134070204 chr3:134070406-134070420
46	EP300	chr3:134069626-134070449	MCF-7	breast:	n/a	chr3:134070194-134070204 chr3:134070406-134070420

No.	Distal block	Cell Line	Cell type
1	chr3:134068339..134071562-chr3:134203031..134205941,6	MCF-7	breast:
2	chr3:134019644..134021494-chr3:134068815..134070339,2	MCF-7	breast:
3	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
4	chr3:134066447..134072766-chr3:134202428..134206376,9	MCF-7	breast:
5	chr3:134046187..134047077-chr3:134069663..134070556,4	MCF-7	breast:
6	chr3:133967562..133971327-chr3:134067822..134072418,4	MCF-7	breast:
7	chr3:134046045..134047071-chr3:134069689..134070482,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260633	TF binding region
ENSG00000163785	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv967066	chr3:134069560-134071258	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:134060800-134072200	Weak transcription	Fetal Kidney	kidney
3	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
4	chr3:134065800-134071400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:134065800-134071400	Enhancers	Fetal Intestine Large	intestine
6	chr3:134065800-134071600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:134065800-134072400	Weak transcription	Spleen	Spleen
8	chr3:134066000-134072800	Enhancers	Duodenum Mucosa	Duodenum
9	chr3:134066200-134071000	Weak transcription	Brain Substantia Nigra	brain
10	chr3:134066400-134071400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:134066400-134071600	Weak transcription	Fetal Lung	lung
12	chr3:134066400-134071600	Enhancers	Placenta	Placenta
13	chr3:134066400-134073000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:134066600-134071800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:134066800-134073000	Weak transcription	Ovary	ovary
17	chr3:134067000-134073400	Enhancers	Pancreas	Pancrea
18	chr3:134067200-134071600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:134067200-134071800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:134067200-134072000	Enhancers	HMEC	breast
21	chr3:134067200-134072800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:134067200-134073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:134067400-134073200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:134067400-134073200	Enhancers	Esophagus	oesophagus
25	chr3:134067600-134072800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:134067600-134073200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
28	chr3:134067800-134072400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:134067800-134073000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:134067800-134073200	Weak transcription	NH-A	brain
31	chr3:134068200-134071000	Weak transcription	NHLF	lung
32	chr3:134068400-134070400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:134068400-134071200	Weak transcription	Fetal Heart	heart
34	chr3:134068400-134072800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:134068400-134073200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:134068400-134074200	Genic enhancers	Fetal Intestine Small	intestine
37	chr3:134068400-134076000	Strong transcription	Fetal Stomach	stomach
38	chr3:134068800-134071800	Enhancers	NHEK	skin
39	chr3:134068800-134073200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:134069000-134072200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:134069000-134074000	Strong transcription	Fetal Brain Female	brain
42	chr3:134069000-134074600	Enhancers	Psoas Muscle	Psoas
43	chr3:134069000-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:134069200-134070400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:134069200-134070400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr3:134069200-134070600	Enhancers	HSMM	muscle
47	chr3:134069200-134071800	Enhancers	HSMMtube	muscle
48	chr3:134069200-134072200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:134069200-134073000	Enhancers	Gastric	stomach
50	chr3:134069200-134074600	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links