Variant report

Variant	rs372578885
Chromosome Location	chr3:49722024-49722025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr3:49721709-49722307	HepG2	liver:	n/a	n/a
2	USF1	chr3:49721883-49722217	HepG2	liver:	n/a	n/a
3	RXRA	chr3:49721628-49722410	HepG2	liver:	n/a	n/a
4	CTCF	chr3:49721937-49722113	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:49721456-49727648	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:49721900-49722050	GM12875	blood:	n/a	n/a
7	CTCF	chr3:49721985-49722053	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:49717503-49727239	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:49721269-49722516	HepG2	liver:	n/a	n/a
10	TCF12	chr3:49721911-49722188	HepG2	liver:	n/a	n/a
11	CTCF	chr3:49721974-49722093	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:49720128-49724935	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:49718663-49722661	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:49721604-49722097	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr3:49721728-49722496	H1-hESC	embryonic stem cell:	n/a	n/a
16	RXRA	chr3:49721870-49722264	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:49716580-49724829	HepG2	liver:	n/a	n/a
18	CTCF	chr3:49721918-49722121	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:49721979-49722107	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:49721940-49722090	GM12867	blood:	n/a	n/a
21	JUND	chr3:49721387-49723325	HepG2	liver:	n/a	n/a
22	CTCF	chr3:49721900-49722050	GM12864	blood:	n/a	n/a
23	CTCF	chr3:49721980-49722130	HBMEC	blood vessel:	n/a	n/a
24	HEY1	chr3:49721339-49722119	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:49721295-49723518	GM12892	blood:	n/a	n/a
26	CTCF	chr3:49722016-49722026	Kidney_OC	kidney:	n/a	n/a
27	CTCF	chr3:49722024-49722044	K562	blood:	n/a	n/a
28	POLR2A	chr3:49721760-49722612	SK-N-MC	brain:	n/a	n/a
29	CTCF	chr3:49721880-49722030	RPTEC	kidney:	n/a	n/a
30	POLR2A	chr3:49721601-49723433	GM12891	blood:	n/a	n/a
31	POLR2A	chr3:49716518-49723590	HepG2	liver:	n/a	n/a
32	CTCF	chr3:49721988-49722077	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:49721966-49722092	HepG2	liver:	n/a	n/a
34	CTCF	chr3:49722011-49722064	GM10248	blood:	n/a	n/a
35	CTCF	chr3:49721900-49722050	HepG2	liver:	n/a	n/a
36	FOSL2	chr3:49721509-49723262	HepG2	liver:	n/a	n/a
37	CTCF	chr3:49722008-49722053	A549	lung:	n/a	n/a
38	CTCF	chr3:49721980-49722091	MCF-7	breast:	n/a	n/a
39	CTCF	chr3:49721997-49722088	GM12891	blood:	n/a	n/a
40	JUND	chr3:49721925-49722101	HepG2	liver:	n/a	n/a
41	HEY1	chr3:49718256-49727412	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:49721840-49722038	K562	blood:	n/a	n/a
43	POLR2A	chr3:49721241-49724664	GM12892	blood:	n/a	n/a
44	SIN3AK20	chr3:49721810-49722091	HepG2	liver:	n/a	n/a
45	CTCF	chr3:49721821-49722162	K562	blood:	n/a	n/a
46	POLR2A	chr3:49721694-49724714	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:49721746-49722145	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:49721676-49723718	GM12878	blood:	n/a	n/a
49	CTCF	chr3:49721857-49722316	K562	blood:	n/a	n/a
50	CTCF	chr3:49721900-49722050	HEK293	kidney:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
2	chr3:49720877..49722933-chr3:49723247..49725096,3	K562	blood:
3	chr3:49719726..49722448-chr3:49723596..49725872,2	K562	blood:

No data

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000173531	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv11877	chr3:49721171-49727086	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv471425	chr3:49721381-49726196	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv482080	chr3:49721381-49726196	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 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	chr3:49712200-49723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49712800-49722200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:49712800-49722200	Strong transcription	Fetal Stomach	stomach
4	chr3:49712800-49723600	Weak transcription	Right Atrium	heart
5	chr3:49712800-49726200	Weak transcription	Small Intestine	intestine
6	chr3:49713000-49722200	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:49713000-49722400	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr3:49713000-49722400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:49713000-49722600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:49713000-49722800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:49713000-49722800	Strong transcription	Thymus	Thymus
12	chr3:49713000-49723200	Weak transcription	Stomach Mucosa	stomach
13	chr3:49713000-49723400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:49713000-49723800	Weak transcription	Fetal Heart	heart
15	chr3:49713200-49722200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:49713200-49722200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:49713200-49722200	Strong transcription	Placenta	Placenta
18	chr3:49713200-49722400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:49713200-49722400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:49713200-49722400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:49713200-49722400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:49713200-49722400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:49713200-49722600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:49713200-49722600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:49713200-49722600	Strong transcription	Brain Germinal Matrix	brain
26	chr3:49713200-49722800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:49713200-49723000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:49713200-49723000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:49713400-49722200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:49713400-49722200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:49713400-49722400	Strong transcription	Adipose Nuclei	Adipose
32	chr3:49713400-49722400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:49713400-49722400	Strong transcription	Fetal Brain Female	brain
34	chr3:49713400-49722600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:49713400-49722800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:49713400-49723000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:49713600-49722200	Strong transcription	Esophagus	oesophagus
38	chr3:49713600-49722400	Strong transcription	Ovary	ovary
39	chr3:49713800-49722400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:49713800-49722400	Strong transcription	Brain Hippocampus Middle	brain
41	chr3:49713800-49723000	Strong transcription	Fetal Intestine Small	intestine
42	chr3:49714000-49723200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:49714200-49722200	Strong transcription	Fetal Intestine Large	intestine
44	chr3:49714200-49722400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:49714200-49723000	Strong transcription	Gastric	stomach
46	chr3:49714200-49723200	Strong transcription	Dnd41	blood
47	chr3:49714600-49722400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:49714600-49723800	Strong transcription	Liver	Liver
49	chr3:49714800-49722400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:49715000-49722200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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