Variant report

Variant	rs374877579
Chromosome Location	chr3:52443652-52443653
allele	A/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	POLR2A	chr3:52443621-52444168	GM12878	blood:	n/a	n/a
2	HCFC1	chr3:52443600-52446586	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:52443366-52445470	K562	blood:	n/a	n/a
4	MXI1	chr3:52443508-52445697	IMR90	lung:	n/a	n/a
5	RCOR1	chr3:52443055-52444488	IMR90	lung:	n/a	n/a
6	MAX	chr3:52443644-52443880	K562	blood:	n/a	n/a
7	MAZ	chr3:52443249-52445513	IMR90	lung:	n/a	n/a
8	POLR2A	chr3:52443341-52444162	H1-hESC	embryonic stem cell:	n/a	n/a
9	HCFC1	chr3:52443617-52445018	K562	blood:	n/a	n/a
10	NRF1	chr3:52443480-52443660	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:52443651-52445324	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:52443645-52444156	SK-N-MC	brain:	n/a	n/a
13	SIN3A	chr3:52443558-52445611	H1-hESC	embryonic stem cell:	n/a	n/a
14	MXI1	chr3:52443027-52445926	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr3:52443620-52443770	HBMEC	blood vessel:	n/a	n/a
16	PML	chr3:52443594-52444162	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:52443447-52445445	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:52443644-52444171	IMR90	lung:	n/a	n/a
19	MTA3	chr3:52442995-52444180	GM12878	blood:	n/a	n/a
20	ESRRA	chr3:52442736-52445785	GM12878	blood:	n/a	chr3:52444629-52444645 chr3:52443225-52443237 chr3:52443981-52443994 chr3:52444631-52444641 chr3:52445485-52445504
21	POLR2A	chr3:52443619-52444173	Hela-S3	cervix:	n/a	n/a
22	CREB1	chr3:52443496-52444942	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:52443346-52446229	HepG2	liver:	n/a	n/a
24	CREB1	chr3:52443537-52444867	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr3:52443512-52445409	GM12878	blood:	n/a	n/a
26	ZNF143	chr3:52443638-52443677	K562	blood:	n/a	n/a
27	CREB1	chr3:52443521-52444316	A549	lung:	n/a	n/a
28	POLR2A	chr3:52443603-52444156	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:52443510-52444186	K562	blood:	n/a	n/a
30	POLR2A	chr3:52443513-52444163	GM12878	blood:	n/a	n/a
31	ELF1	chr3:52443635-52445037	GM12878	blood:	n/a	chr3:52444534-52444546 chr3:52444834-52444843 chr3:52444802-52444814
32	MAX	chr3:52443501-52445541	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:52443584-52444138	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:52443641-52445008	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:52443546-52444190	HL-60	blood:	n/a	n/a
36	POLR2A	chr3:52443593-52444976	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr3:52443652-52444419	GM12878	blood:	n/a	n/a
38	REST	chr3:52443152-52446007	H1-neurons	neurons:	n/a	chr3:52443163-52443176 chr3:52443304-52443317 chr3:52444795-52444805
39	POLR2A	chr3:52443646-52445663	H1-neurons	neurons:	n/a	n/a
40	CREB1	chr3:52443391-52445114	HepG2	liver:	n/a	n/a
41	MAZ	chr3:52443641-52444937	K562	blood:	n/a	n/a
42	ATF1	chr3:52443561-52444243	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
2	chr3:52442610..52445343-chr3:52803282..52805357,2	K562	blood:
3	chr3:52324588..52327004-chr3:52442941..52444727,2	MCF-7	breast:
4	chr3:52311359..52313564-chr3:52443173..52445594,2	MCF-7	breast:
5	chr3:52015943..52018006-chr3:52443224..52445803,2	K562	blood:
6	chr3:52271478..52274801-chr3:52443057..52446273,4	K562	blood:
7	chr3:52442891..52445847-chr3:52570573..52572369,2	K562	blood:
8	chr3:52272619..52275147-chr3:52443057..52446254,5	K562	blood:
9	chr3:52443115..52446014-chr3:52718098..52719635,2	K562	blood:

Variant related genes	Relation type
PHF7	TF binding region
BAP1	TF binding region
ENSG00000243224	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv3325653	chr3:52442937-52445885	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3354699	chr3:52443212-52445760	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3407957	chr3:52443512-52445260	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52442400-52443800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr3:52442400-52445200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:52442600-52443800	Flanking Active TSS	Fetal Brain Male	brain
4	chr3:52442600-52443800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr3:52442600-52445800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:52442800-52443800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:52442800-52443800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr3:52442800-52443800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:52442800-52443800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:52442800-52443800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr3:52442800-52443800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
12	chr3:52442800-52445200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr3:52442800-52446400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:52443000-52443800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:52443000-52443800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:52443000-52443800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr3:52443000-52443800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr3:52443000-52443800	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr3:52443000-52443800	Flanking Active TSS	Liver	Liver
20	chr3:52443000-52443800	Flanking Active TSS	Placenta	Placenta
21	chr3:52443000-52443800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:52443000-52443800	Flanking Active TSS	Right Ventricle	heart
23	chr3:52443000-52443800	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr3:52443000-52445600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr3:52443200-52443800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr3:52443200-52443800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:52443200-52443800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr3:52443200-52443800	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr3:52443200-52443800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr3:52443200-52443800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr3:52443200-52443800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:52443200-52443800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:52443200-52443800	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr3:52443200-52443800	Flanking Active TSS	Fetal Thymus	thymus
35	chr3:52443200-52445000	Active TSS	Placenta Amnion	Placenta Amnion
36	chr3:52443200-52445200	Active TSS	A549	lung
37	chr3:52443200-52445400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:52443200-52445600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:52443200-52445600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:52443200-52445600	Active TSS	Gastric	stomach
41	chr3:52443200-52445800	Active TSS	Ovary	ovary
42	chr3:52443200-52446200	Active TSS	K562	blood
43	chr3:52443400-52443800	Flanking Active TSS	Esophagus	oesophagus
44	chr3:52443400-52443800	Bivalent/Poised TSS	HepG2	liver
45	chr3:52443400-52444000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:52443400-52445000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52443400-52445000	Active TSS	Fetal Lung	lung
48	chr3:52443400-52445000	Active TSS	NHEK	skin
49	chr3:52443400-52445000	Active TSS	NHLF	lung
50	chr3:52443400-52445200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links