Variant report

Variant	rs562175606
Chromosome Location	chr3:49968373-49968374
allele	A/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	CTCF	chr3:49968340-49968490	GM12874	blood:	n/a	chr3:49968473-49968486
2	CTCF	chr3:49968360-49968510	HRPEpiC	eye:	n/a	chr3:49968473-49968486
3	HEY1	chr3:49968311-49968680	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:49968364-49968574	HepG2	liver:	n/a	n/a
5	MAX	chr3:49968362-49968562	K562	blood:	n/a	n/a
6	RAD21	chr3:49968248-49968692	H1-hESC	embryonic stem cell:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
7	CTCF	chr3:49968362-49968625	H1-hESC	embryonic stem cell:	n/a	chr3:49968473-49968486
8	POLR2A	chr3:49968330-49968757	HCT-116	colon:	n/a	n/a
9	MYC	chr3:49968335-49968469	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr3:49968300-49968450	BE2_C	brain:	n/a	n/a
11	CTCF	chr3:49968294-49968646	K562	blood:	n/a	chr3:49968473-49968486
12	RAD21	chr3:49968186-49968769	HCT-116	colon:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
13	CTCF	chr3:49968342-49968668	K562	blood:	n/a	chr3:49968473-49968486
14	HEY1	chr3:49968345-49968699	K562	blood:	n/a	n/a
15	EP300	chr3:49968214-49968554	GM12878	blood:	n/a	n/a
16	RAD21	chr3:49968318-49968691	H1-hESC	embryonic stem cell:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
17	TBP	chr3:49968311-49968643	K562	blood:	n/a	n/a
18	POLR2A	chr3:49968251-49968800	K562	blood:	n/a	n/a
19	POLR2A	chr3:49968368-49968706	K562	blood:	n/a	n/a
20	RAD21	chr3:49968265-49968701	HepG2	liver:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
21	ZNF143	chr3:49968338-49968667	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr3:49968310-49968664	H1-hESC	embryonic stem cell:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
23	YY1	chr3:49968335-49968667	HepG2	liver:	n/a	n/a
24	MXI1	chr3:49966578-49969002	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr3:49968340-49968490	GM12872	blood:	n/a	chr3:49968473-49968486
26	RAD21	chr3:49968372-49968642	HepG2	liver:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
27	CTCF	chr3:49968271-49968671	HepG2	liver:	n/a	chr3:49968473-49968486
28	RAD21	chr3:49968328-49968651	Hela-S3	cervix:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
29	RAD21	chr3:49968348-49968643	SK-N-SH_RA	brain:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
30	ZNF384	chr3:49968278-49968665	K562	blood:	n/a	n/a
31	POLR2A	chr3:49968370-49968701	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:49968306-49968703	K562	blood:	n/a	chr3:49968473-49968486
33	RAD21	chr3:49968269-49968661	ECC-1	luminal epithelium:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484

No.	Distal block	Cell Line	Cell type
1	chr3:49892535..49894935-chr3:49965699..49968471,2	K562	blood:
2	chr3:49965505..49970003-chr3:49975811..49980300,11	K562	blood:
3	chr3:49964076..49966567-chr3:49968283..49970694,2	K562	blood:
4	chr3:49840341..49842910-chr3:49967049..49969753,2	K562	blood:
5	chr3:49965568..49971141-chr3:49975411..49979217,7	MCF-7	breast:
6	chr3:49966957..49970009-chr3:49975972..49978983,5	MCF-7	breast:
7	chr3:49965505..49970003-chr3:49974970..49980028,17	K562	blood:
8	chr3:49966031..49968659-chr3:50125180..50127794,3	K562	blood:
9	chr3:49750537..49752087-chr3:49966182..49968764,2	K562	blood:
10	chr3:49966762..49969614-chr3:50125142..50129125,3	K562	blood:

Variant related genes	Relation type
MON1A	TF binding region
ENSG00000164068	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000183763	Chromatin interaction
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv965334	chr3:49967342-50000012	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49967600-49968400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49967600-49968400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:49967600-49968400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:49967600-49968400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:49967600-49968400	Weak transcription	Spleen	Spleen
6	chr3:49967600-49968800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:49967600-49969000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:49967600-49969200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:49967600-49969200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:49967600-49977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49967800-49968400	Enhancers	Brain Substantia Nigra	brain
12	chr3:49967800-49968600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:49967800-49968600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:49967800-49968600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:49967800-49968600	Enhancers	Fetal Muscle Leg	muscle
16	chr3:49967800-49968600	Enhancers	Placenta	Placenta
17	chr3:49967800-49968600	Enhancers	Fetal Thymus	thymus
18	chr3:49967800-49968600	Enhancers	Left Ventricle	heart
19	chr3:49967800-49968600	Enhancers	Stomach Mucosa	stomach
20	chr3:49967800-49968600	Enhancers	A549	lung
21	chr3:49967800-49968600	Enhancers	GM12878-XiMat	blood
22	chr3:49967800-49968800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:49967800-49968800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:49967800-49968800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:49967800-49968800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:49967800-49968800	Enhancers	Hela-S3	cervix
27	chr3:49967800-49969000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:49967800-49969000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49967800-49969000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:49967800-49969000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:49967800-49969000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:49967800-49969000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr3:49967800-49969000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:49967800-49969000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:49967800-49969000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:49967800-49969000	Enhancers	NHEK	skin
37	chr3:49967800-49969800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:49967800-49971000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:49967800-49971200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:49967800-49977000	Weak transcription	Primary B cells from cord blood	blood
41	chr3:49967800-49977000	Weak transcription	NHLF	lung
42	chr3:49968000-49968400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:49968000-49968400	Weak transcription	Psoas Muscle	Psoas
44	chr3:49968000-49968600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:49968000-49968600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:49968000-49968600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr3:49968000-49968800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:49968000-49968800	Enhancers	Pancreas	Pancrea
49	chr3:49968000-49968800	Enhancers	Rectal Smooth Muscle	rectum
50	chr3:49968000-49968800	Enhancers	Right Atrium	heart

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