Variant report

Variant	rs550410537
Chromosome Location	chr3:49968435-49968436
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	CTCF	chr3:49968380-49968530	K562	blood:	n/a	chr3:49968473-49968486
2	CTCF	chr3:49968340-49968490	GM12874	blood:	n/a	chr3:49968473-49968486
3	CTCF	chr3:49968420-49968570	HepG2	liver:	n/a	chr3:49968473-49968486
4	JUND	chr3:49968384-49968841	K562	blood:	n/a	n/a
5	CTCF	chr3:49968360-49968510	HRPEpiC	eye:	n/a	chr3:49968473-49968486
6	CTCF	chr3:49968400-49968550	GM06990	blood:	n/a	chr3:49968473-49968486
7	CTCF	chr3:49968392-49968594	K562	blood:	n/a	chr3:49968473-49968486
8	HEY1	chr3:49968311-49968680	HepG2	liver:	n/a	n/a
9	GTF2B	chr3:49968426-49968626	K562	blood:	n/a	n/a
10	POLR2A	chr3:49968364-49968574	HepG2	liver:	n/a	n/a
11	MAX	chr3:49968362-49968562	K562	blood:	n/a	n/a
12	RAD21	chr3:49968248-49968692	H1-hESC	embryonic stem cell:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
13	CTCF	chr3:49968380-49968530	SK-N-SH_RA	brain:	n/a	chr3:49968473-49968486
14	POLR2A	chr3:49968420-49968719	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:49968362-49968625	H1-hESC	embryonic stem cell:	n/a	chr3:49968473-49968486
16	POLR2A	chr3:49968330-49968757	HCT-116	colon:	n/a	n/a
17	POLR2A	chr3:49968432-49968672	Hela-S3	cervix:	n/a	n/a
18	MYC	chr3:49968335-49968469	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr3:49968400-49968550	Hela-S3	cervix:	n/a	chr3:49968473-49968486
20	CTCF	chr3:49968420-49968570	RPTEC	kidney:	n/a	chr3:49968473-49968486
21	CTCF	chr3:49968300-49968450	BE2_C	brain:	n/a	n/a
22	CTCF	chr3:49968294-49968646	K562	blood:	n/a	chr3:49968473-49968486
23	RAD21	chr3:49968186-49968769	HCT-116	colon:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
24	CTCF	chr3:49968342-49968668	K562	blood:	n/a	chr3:49968473-49968486
25	RAD21	chr3:49968389-49968592	HepG2	liver:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
26	CTCF	chr3:49968400-49968550	BJ	skin:	n/a	chr3:49968473-49968486
27	CTCF	chr3:49968380-49968530	HCT-116	colon:	n/a	chr3:49968473-49968486
28	HEY1	chr3:49968345-49968699	K562	blood:	n/a	n/a
29	CTCF	chr3:49968385-49968595	K562	blood:	n/a	chr3:49968473-49968486
30	EP300	chr3:49968214-49968554	GM12878	blood:	n/a	n/a
31	SMC3	chr3:49968383-49968616	HepG2	liver:	n/a	chr3:49968472-49968486
32	POLR2A	chr3:49968398-49968706	K562	blood:	n/a	n/a
33	RAD21	chr3:49968318-49968691	H1-hESC	embryonic stem cell:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
34	TBP	chr3:49968311-49968643	K562	blood:	n/a	n/a
35	MAX	chr3:49968381-49968633	K562	blood:	n/a	n/a
36	POLR2A	chr3:49968251-49968800	K562	blood:	n/a	n/a
37	RAD21	chr3:49968397-49968739	ECC-1	luminal epithelium:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
38	CTCF	chr3:49968380-49968530	MCF-7	breast:	n/a	chr3:49968473-49968486
39	POLR2A	chr3:49968368-49968706	K562	blood:	n/a	n/a
40	RAD21	chr3:49968265-49968701	HepG2	liver:	n/a	chr3:49968474-49968487 chr3:49968476-49968486 chr3:49968475-49968484
41	CTCF	chr3:49968400-49968550	HRE	kidney:	n/a	chr3:49968473-49968486
42	CTCF	chr3:49968408-49968553	LNCaP	prostate:	n/a	chr3:49968473-49968486
43	USF2	chr3:49968433-49968622	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:49968418-49968474	HepG2	liver:	n/a	n/a
45	CTCF	chr3:49968420-49968570	HCT-116	colon:	n/a	chr3:49968473-49968486
46	ZNF143	chr3:49968338-49968667	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr3:49968408-49968569	Hela-S3	cervix:	n/a	chr3:49968473-49968486
48	GTF2F1	chr3:49968393-49968593	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr3:49968400-49968550	BE2_C	brain:	n/a	chr3:49968473-49968486
50	RAD21	chr3:49968310-49968664	H1-hESC	embryonic stem cell:	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
ENSG00000183763	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000004534	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000003756	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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49967600-49968800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49967600-49969000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:49967600-49969200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:49967600-49969200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:49967600-49977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:49967800-49968600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:49967800-49968600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:49967800-49968600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:49967800-49968600	Enhancers	Fetal Muscle Leg	muscle
10	chr3:49967800-49968600	Enhancers	Placenta	Placenta
11	chr3:49967800-49968600	Enhancers	Fetal Thymus	thymus
12	chr3:49967800-49968600	Enhancers	Left Ventricle	heart
13	chr3:49967800-49968600	Enhancers	Stomach Mucosa	stomach
14	chr3:49967800-49968600	Enhancers	A549	lung
15	chr3:49967800-49968600	Enhancers	GM12878-XiMat	blood
16	chr3:49967800-49968800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:49967800-49968800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:49967800-49968800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:49967800-49968800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:49967800-49968800	Enhancers	Hela-S3	cervix
21	chr3:49967800-49969000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:49967800-49969000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49967800-49969000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:49967800-49969000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:49967800-49969000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:49967800-49969000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:49967800-49969000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:49967800-49969000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:49967800-49969000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:49967800-49969000	Enhancers	NHEK	skin
31	chr3:49967800-49969800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:49967800-49971000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:49967800-49971200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:49967800-49977000	Weak transcription	Primary B cells from cord blood	blood
35	chr3:49967800-49977000	Weak transcription	NHLF	lung
36	chr3:49968000-49968600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:49968000-49968600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:49968000-49968600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr3:49968000-49968800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:49968000-49968800	Enhancers	Pancreas	Pancrea
41	chr3:49968000-49968800	Enhancers	Rectal Smooth Muscle	rectum
42	chr3:49968000-49968800	Enhancers	Right Atrium	heart
43	chr3:49968000-49968800	Flanking Active TSS	K562	blood
44	chr3:49968000-49969200	Enhancers	Fetal Kidney	kidney
45	chr3:49968000-49969400	Enhancers	Fetal Intestine Large	intestine
46	chr3:49968000-49976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:49968200-49968800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:49968200-49968800	Enhancers	Adipose Nuclei	Adipose
49	chr3:49968200-49968800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:49968200-49968800	Flanking Active TSS	HepG2	liver

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