Variant report

Variant	rs373875132
Chromosome Location	chr3:142682034-142682035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr3:142681849-142682212	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr3:142681752-142682086	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr3:142681914-142683570	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr3:142681583-142683285	PBDE	blood:	n/a	n/a
5	SETDB1	chr3:142680934-142682173	K562	blood:	n/a	n/a
6	TAF1	chr3:142681826-142682870	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr3:142681242-142682221	H1-hESC	embryonic stem cell:	n/a	n/a
8	HMGN3	chr3:142681685-142683281	K562	blood:	n/a	n/a
9	TAF1	chr3:142681780-142682155	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr3:142681836-142682096	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr3:142681486-142682063	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr3:142681778-142682048	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr3:142681850-142682987	HepG2	liver:	n/a	chr3:142682537-142682551 chr3:142682773-142682787 chr3:142682770-142682779 chr3:142682542-142682553 chr3:142682543-142682557 chr3:142682548-142682557 chr3:142682745-142682759 chr3:142682709-142682723 chr3:142682539-142682550 chr3:142682542-142682551 chr3:142682715-142682729 chr3:142682545-142682554
14	ZNF143	chr3:142681826-142682078	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr3:142681102-142682892	H1-hESC	embryonic stem cell:	n/a	chr3:142682194-142682208 chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
16	MAX	chr3:142681255-142682199	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr3:142681257-142683103	A549	lung:	n/a	chr3:142682825-142682834
18	POLR2A	chr3:142681737-142683308	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F6	chr3:142681208-142682147	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr3:142682016-142683054	A549	lung:	n/a	chr3:142682825-142682834
21	REST	chr3:142681752-142682066	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr3:142682025-142682346	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142681996-142682046	NHDF-neo	bronchial:	n/a
2	chr3:142681996-142682046	PANC-1	pancreas:	n/a
3	chr3:142681996-142682046	SKMC	muscle:	n/a
4	chr3:142681996-142682046	ECC-1	luminal epithelium:	n/a
5	chr3:142681996-142682046	NB4	blood:	n/a
6	chr3:142681996-142682046	Hela-S3	cervix:	n/a
7	chr3:142681996-142682046	HCM	heart:	n/a
8	chr3:142681996-142682046	SK-N-SH_RA	brain:	n/a
9	chr3:142681996-142682046	AG09309	skin:	n/a
10	chr3:142681996-142682046	SK-N-MC	brain:	n/a
11	chr3:142681996-142682046	HMEC	breast:	n/a
12	chr3:142681996-142682046	GM12891	blood:	n/a
13	chr3:142681996-142682046	HEK293	kidney:	embryo
14	chr3:142681996-142682046	PrEC	prostate:	n/a
15	chr3:142681996-142682046	HRE	kidney:	n/a
16	chr3:142681996-142682046	GM06990	blood:	n/a
17	chr3:142681996-142682046	IMR90	lung:	fetal
18	chr3:142681996-142682046	AG09319	gingival:	n/a
19	chr3:142681996-142682046	AG04449	skin:	fetal
20	chr3:142681996-142682046	MCF10A-Er-Src	breast:	n/a
21	chr3:142681996-142682046	ovcar-3	ovarian:	n/a
22	chr3:142681996-142682046	PFSK-1	brain:	n/a
23	chr3:142681996-142682046	NH-A	brain:	n/a
24	chr3:142681996-142682046	BE2_C	brain:	n/a
25	chr3:142681996-142682046	HPAEpiC	pulmonary alveolar:	n/a
26	chr3:142681996-142682046	A549	lung:	n/a
27	chr3:142681996-142682046	HCF	heart:	n/a
28	chr3:142681996-142682046	HepG2	liver:	n/a
29	chr3:142681996-142682046	U87	brain:	n/a
30	chr3:142681996-142682046	AoSMC	blood vessel:	n/a
31	chr3:142681996-142682046	HNPCEpiC	eye:	n/a
32	chr3:142681996-142682046	H1-hESC	embryonic stem cell:	embryo
33	chr3:142681996-142682046	HL-60	blood:	n/a
34	chr3:142681996-142682046	GM19239	blood:	n/a
35	chr3:142681996-142682046	SK-N-SH	brain:	n/a
36	chr3:142681996-142682046	Caco-2	colon:	n/a
37	chr3:142681996-142682046	BJ	skin:	n/a
38	chr3:142681996-142682046	HIPEpiC	eye:	n/a
39	chr3:142681996-142682046	LNCaP	prostate:	n/a
40	chr3:142681996-142682046	HRPEpiC	eye:	n/a
41	chr3:142681996-142682046	AG10803	skin:	n/a
42	chr3:142681996-142682046	GM12892	blood:	n/a
43	chr3:142681996-142682046	GM12878	blood:	n/a
44	chr3:142681996-142682046	MCF-7	breast:	n/a
45	chr3:142681996-142682046	HRCEpiC	kidney:	n/a
46	chr3:142681996-142682046	RPTEC	kidney:	n/a
47	chr3:142681996-142682046	Jurkat	blood:	n/a
48	chr3:142681996-142682046	HCPEpiC	choroid plexus:	n/a
49	chr3:142681996-142682046	NT2-D1	testis:	n/a
50	chr3:142681996-142682046	HCT-116	colon:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142681877..142683958-chr3:142718843..142721049,2	K562	blood:
2	chr3:142296891..142299259-chr3:142680803..142682548,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241570	TF binding region
U2SURP	TF binding region
PAQR9	TF binding region
U2SURP	CpG island
PAQR9	CpG island
ENSG00000241570	CpG island
ENSG00000268129	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000163714	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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv3443662	chr3:142681287-142684135	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	esv3388028	chr3:142681537-142683935	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142681000-142683600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:142681200-142682200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:142681400-142682200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:142681400-142683400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr3:142681400-142683400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:142681400-142683600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:142681400-142683600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:142681400-142683600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:142681600-142682200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:142681600-142682200	Bivalent Enhancer	Lung	lung
11	chr3:142681600-142682200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
12	chr3:142681600-142682400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:142681600-142682600	Bivalent Enhancer	Placenta	Placenta
14	chr3:142681600-142683000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr3:142681600-142683000	Active TSS	Psoas Muscle	Psoas
16	chr3:142681600-142683200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
17	chr3:142681600-142683400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:142681600-142683400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
19	chr3:142681600-142683400	Bivalent/Poised TSS	NHEK	skin
20	chr3:142681600-142683600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr3:142681600-142683600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:142681600-142683800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:142681800-142682200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:142681800-142682200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
25	chr3:142681800-142682200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:142681800-142682200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:142681800-142682200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:142681800-142682200	Bivalent Enhancer	Fetal Stomach	stomach
29	chr3:142681800-142682200	Bivalent Enhancer	Fetal Thymus	thymus
30	chr3:142681800-142682200	Flanking Active TSS	Right Atrium	heart
31	chr3:142681800-142682200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr3:142681800-142682200	Enhancers	K562	blood
33	chr3:142681800-142682200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr3:142681800-142682400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
35	chr3:142681800-142682400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:142681800-142682400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:142681800-142682600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
38	chr3:142681800-142682800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr3:142681800-142682800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:142681800-142683000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:142681800-142683000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
42	chr3:142681800-142683000	Bivalent/Poised TSS	HSMM	muscle
43	chr3:142681800-142683000	Bivalent/Poised TSS	HUVEC	blood vessel
44	chr3:142681800-142683200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:142681800-142683200	Active TSS	Fetal Brain Female	brain
46	chr3:142681800-142683400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:142681800-142683400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:142681800-142683400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
49	chr3:142681800-142683400	Active TSS	Brain Angular Gyrus	brain
50	chr3:142681800-142683400	Bivalent/Poised TSS	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links