Variant report

Variant	rs555734986
Chromosome Location	chr4:99064434-99064435
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	chr4:99064322-99064971	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr4:99063986-99064521	ECC-1	luminal epithelium:	n/a	n/a
3	IRF1	chr4:99064419-99064619	K562	blood:	n/a	n/a
4	PML	chr4:99064074-99065122	GM12878	blood:	n/a	n/a
5	POU2F2	chr4:99064371-99064964	GM12878	blood:	n/a	n/a
6	KAP1	chr4:99063916-99064996	HEK293	kidney:	n/a	n/a
7	POLR2A	chr4:99064353-99064980	GM12891	blood:	n/a	n/a
8	MAX	chr4:99064009-99065140	ECC-1	luminal epithelium:	n/a	n/a
9	RCOR1	chr4:99064196-99064869	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:99064333-99065027	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr4:99063862-99065121	U87	brain:	n/a	n/a
12	ELF1	chr4:99064083-99065049	HepG2	liver:	n/a	chr4:99064479-99064490
13	MTA3	chr4:99063877-99064632	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:99063780-99065230	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:99064039-99065119	GM12892	blood:	n/a	n/a
16	GATA1	chr4:99063077-99065020	PBDE	blood:	n/a	chr4:99063116-99063126 chr4:99063382-99063392 chr4:99063383-99063392 chr4:99063381-99063393 chr4:99063383-99063390 chr4:99063379-99063395
17	CTCF	chr4:99064034-99064471	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr4:99063994-99064492	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr4:99063963-99064902	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr4:99064156-99064893	HepG2	liver:	n/a	n/a
21	ELF1	chr4:99063899-99065180	HCT-116	colon:	n/a	chr4:99064479-99064490
22	POLR2A	chr4:99063932-99065015	GM12892	blood:	n/a	n/a
23	CTCF	chr4:99064085-99064445	K562	blood:	n/a	n/a
24	POLR2A	chr4:99064290-99064993	IMR90	lung:	n/a	n/a
25	TCF7L2	chr4:99064097-99065011	Hela-S3	cervix:	n/a	n/a
26	MAX	chr4:99064039-99065062	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZEB1	chr4:99063947-99065159	HepG2	liver:	n/a	n/a
28	TAF1	chr4:99064002-99065165	ECC-1	luminal epithelium:	n/a	n/a
29	POU2F2	chr4:99064342-99064963	GM12891	blood:	n/a	n/a
30	POLR2A	chr4:99064351-99064939	H1-hESC	embryonic stem cell:	n/a	n/a
31	TBP	chr4:99063849-99065024	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr4:99064359-99064709	PFSK-1	brain:	n/a	n/a
33	CTCF	chr4:99063927-99064823	HCT-116	colon:	n/a	n/a
34	POLR2A	chr4:99063900-99065181	MCF-7	breast:	n/a	n/a
35	JUND	chr4:99064066-99064976	H1-hESC	embryonic stem cell:	n/a	n/a
36	EBF1	chr4:99064401-99064921	GM12878	blood:	n/a	chr4:99064678-99064689 chr4:99064701-99064712
37	ZNF143	chr4:99064108-99064803	H1-hESC	embryonic stem cell:	n/a	chr4:99064317-99064327
38	CTCF	chr4:99064065-99064515	MCF-7	breast:	n/a	n/a
39	POLR2A	chr4:99064148-99064993	HL-60	blood:	n/a	n/a
40	KAP1	chr4:99064008-99065043	U2OS	brain:	n/a	n/a
41	CTCF	chr4:99064067-99064478	IMR90	lung:	n/a	n/a
42	MYC	chr4:99064077-99064511	H1-hESC	embryonic stem cell:	n/a	n/a
43	SRF	chr4:99064297-99064862	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr4:99064112-99064513	GM19238	blood:	n/a	n/a
45	ZNF143	chr4:99064117-99064747	Hela-S3	cervix:	n/a	chr4:99064317-99064327
46	REST	chr4:99064412-99065107	A549	lung:	n/a	chr4:99064601-99064621 chr4:99064601-99064621 chr4:99064604-99064617
47	YY1	chr4:99064126-99064955	GM12878	blood:	n/a	n/a
48	SP1	chr4:99064137-99064851	A549	lung:	n/a	chr4:99064440-99064450 chr4:99064628-99064640 chr4:99064439-99064450 chr4:99064628-99064640
49	MAX	chr4:99063748-99065111	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:99064223-99065107	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99063959..99066263-chr4:99181971..99183968,2	K562	blood:
2	chr4:99062262..99068404-chr4:99178848..99183768,9	MCF-7	breast:

Variant related genes	Relation type
STPG2	TF binding region
ENSG00000214559	Chromatin interaction
ENSG00000138698	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879643	chr4:98317295-99065480	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1002098	chr4:98501337-99086320	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537193	chr4:98501337-99086320	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv879648	chr4:98547717-99104879	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1000011	chr4:98562308-99101692	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1000956	chr4:98732458-99178588	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv528390	chr4:98873667-99065480	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv879650	chr4:99057457-99172232	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv998270	chr4:99063275-99120404	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99063400-99064800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr4:99063400-99065200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:99063400-99065600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:99063600-99064800	Active TSS	GM12878-XiMat	blood
5	chr4:99063600-99064800	Active TSS	HMEC	breast
6	chr4:99063600-99065200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:99063600-99065200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:99063600-99065200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:99063600-99065200	Active TSS	Brain Germinal Matrix	brain
10	chr4:99063800-99064600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:99063800-99064800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:99063800-99064800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:99063800-99064800	Active TSS	Thymus	Thymus
14	chr4:99063800-99065000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr4:99063800-99065000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:99063800-99065000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:99063800-99065000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:99063800-99065000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:99063800-99065000	Active TSS	Esophagus	oesophagus
20	chr4:99063800-99065000	Active TSS	Fetal Intestine Large	intestine
21	chr4:99063800-99065000	Active TSS	Placenta Amnion	Placenta Amnion
22	chr4:99063800-99065000	Active TSS	Psoas Muscle	Psoas
23	chr4:99063800-99065000	Active TSS	Stomach Mucosa	stomach
24	chr4:99063800-99065000	Active TSS	A549	lung
25	chr4:99063800-99065200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:99063800-99065200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr4:99063800-99065200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr4:99063800-99065200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:99063800-99065200	Active TSS	Brain Hippocampus Middle	brain
30	chr4:99063800-99065200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr4:99063800-99065200	Active TSS	Brain Substantia Nigra	brain
32	chr4:99063800-99065200	Active TSS	Colonic Mucosa	Colon
33	chr4:99063800-99065200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr4:99063800-99065200	Active TSS	Fetal Kidney	kidney
35	chr4:99063800-99065200	Active TSS	Fetal Stomach	stomach
36	chr4:99063800-99065200	Active TSS	Pancreas	Pancrea
37	chr4:99063800-99065200	Active TSS	Rectal Smooth Muscle	rectum
38	chr4:99063800-99065200	Active TSS	Stomach Smooth Muscle	stomach
39	chr4:99063800-99065400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:99063800-99065400	Active TSS	Right Atrium	heart
41	chr4:99063800-99065600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr4:99063800-99065600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:99064000-99064600	Active TSS	Fetal Muscle Trunk	muscle
44	chr4:99064000-99064800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr4:99064000-99064800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:99064000-99064800	Active TSS	Fetal Brain Male	brain
47	chr4:99064000-99064800	Active TSS	HepG2	liver
48	chr4:99064000-99064800	Active TSS	NHEK	skin
49	chr4:99064000-99065000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:99064000-99065000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links