Variant report

Variant	rs540422916
Chromosome Location	chr9:94903657-94903658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:94903639-94903770	MCF-7	breast:	n/a	n/a
2	CTCF	chr9:94903620-94903762	MCF-7	breast:	n/a	n/a
3	CTCF	chr9:94903640-94903790	GM12869	blood:	n/a	n/a
4	CTCF	chr9:94903596-94903795	HepG2	liver:	n/a	n/a
5	CTCF	chr9:94903600-94903750	HMF	breast:	n/a	n/a
6	MXI1	chr9:94902467-94903909	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr9:94903640-94903790	GM12867	blood:	n/a	n/a
8	CTCF	chr9:94903580-94903730	HMEC	breast:	n/a	n/a
9	RAD21	chr9:94903389-94903880	IMR90	lung:	n/a	n/a
10	CTCF	chr9:94903560-94903710	RPTEC	kidney:	n/a	n/a
11	CTCF	chr9:94903624-94903741	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr9:94903620-94903770	GM12865	blood:	n/a	n/a
13	CTCF	chr9:94903600-94903750	AG04449	skin:	n/a	n/a
14	CTCF	chr9:94903552-94903857	IMR90	lung:	n/a	n/a
15	CTCF	chr9:94903600-94903750	HEK293	kidney:	n/a	n/a
16	CTCF	chr9:94903540-94903690	GM12868	blood:	n/a	n/a
17	CTCF	chr9:94903641-94903665	GM13976	blood:	n/a	n/a
18	NRF1	chr9:94903455-94904371	SK-N-SH	brain:	n/a	chr9:94904230-94904239
19	CTCF	chr9:94903580-94903730	GM12874	blood:	n/a	n/a
20	CTCF	chr9:94903600-94903750	HUVEC	blood vessel:	n/a	n/a
21	GABPA	chr9:94903449-94903828	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr9:94903560-94903710	HEEpiC	esophagus:	n/a	n/a
23	CTCF	chr9:94903651-94903756	Pancreas_OC	pancreas:	n/a	n/a
24	CTCF	chr9:94903560-94903710	HCFaa	heart:	n/a	n/a
25	CTCF	chr9:94903620-94903770	GM12871	blood:	n/a	n/a
26	MAX	chr9:94903499-94904075	MCF-7	breast:	n/a	n/a
27	MXI1	chr9:94902085-94904234	IMR90	lung:	n/a	n/a
28	CTCF	chr9:94903600-94903750	HepG2	liver:	n/a	n/a
29	CTCF	chr9:94903640-94903790	AoAF	blood vessel:	n/a	n/a
30	CTCF	chr9:94903560-94903710	AG04449	skin:	n/a	n/a
31	PAX5	chr9:94903539-94903825	GM12892	blood:	n/a	n/a
32	CTCF	chr9:94903600-94903750	SK-N-SH_RA	brain:	n/a	n/a
33	NRF1	chr9:94903555-94903765	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr9:94903574-94903884	IMR90	lung:	n/a	n/a
35	HA-E2F1	chr9:94903316-94904114	MCF-7	breast:	n/a	n/a
36	CTCF	chr9:94903600-94903750	HCM	heart:	n/a	n/a
37	CTCF	chr9:94903585-94903770	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr9:94903620-94903770	AG09319	gingival:	n/a	n/a
39	USF1	chr9:94903525-94903821	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr9:94903640-94903790	GM12870	blood:	n/a	n/a
41	CTCF	chr9:94903630-94903747	LNCaP	prostate:	n/a	n/a
42	ZNF143	chr9:94903540-94903804	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr9:94903560-94903710	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr9:94903560-94903710	GM12873	blood:	n/a	n/a
45	RAD21	chr9:94903506-94903816	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr9:94903600-94903750	HPAF	blood vessel:	n/a	n/a
47	CTCF	chr9:94903580-94903730	HA-sp	spinal cord:	n/a	n/a
48	CTCF	chr9:94903620-94903770	MCF-7	breast:	n/a	n/a
49	CTCF	chr9:94903620-94903770	SK-N-SH_RA	brain:	n/a	n/a
50	CTCF	chr9:94903580-94903730	GM12875	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
2	chr9:94901685..94904988-chr9:95003695..95006795,3	MCF-7	breast:
3	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
4	chr9:94902223..94905302-chr9:94908199..94910430,4	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000225511	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000196305	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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972778	chr9:94902068-94908273	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94902200-94904200	Enhancers	Liver	Liver
2	chr9:94902800-94903800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:94902800-94903800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
4	chr9:94902800-94904000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:94902800-94904000	Enhancers	Primary hematopoietic stem cells	blood
6	chr9:94902800-94904000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
7	chr9:94902800-94904000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:94902800-94904000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
9	chr9:94902800-94904200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:94902800-94904200	Active TSS	Fetal Kidney	kidney
11	chr9:94902800-94904200	Enhancers	Lung	lung
12	chr9:94903000-94903800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:94903000-94903800	Bivalent Enhancer	Fetal Heart	heart
14	chr9:94903000-94904000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:94903000-94904000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:94903000-94904000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
17	chr9:94903000-94904000	Bivalent Enhancer	Spleen	Spleen
18	chr9:94903000-94904800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr9:94903200-94903800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
20	chr9:94903200-94903800	Bivalent Enhancer	Stomach Mucosa	stomach
21	chr9:94903200-94904000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:94903200-94904000	Bivalent Enhancer	Primary B cells from cord blood	blood
23	chr9:94903200-94904000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
24	chr9:94903200-94904000	Flanking Active TSS	HMEC	breast
25	chr9:94903200-94904200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr9:94903200-94904200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr9:94903200-94904200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:94903200-94904200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:94903200-94904200	Enhancers	Gastric	stomach
30	chr9:94903400-94903800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:94903400-94903800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:94903400-94903800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr9:94903400-94903800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:94903400-94903800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr9:94903400-94903800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr9:94903400-94903800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:94903400-94903800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr9:94903400-94903800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:94903400-94903800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:94903400-94903800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:94903400-94903800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
42	chr9:94903400-94903800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr9:94903400-94903800	Active TSS	Esophagus	oesophagus
44	chr9:94903400-94903800	Bivalent/Poised TSS	Fetal Brain Female	brain
45	chr9:94903400-94903800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr9:94903400-94903800	Bivalent/Poised TSS	Left Ventricle	heart
47	chr9:94903400-94903800	Active TSS	Ovary	ovary
48	chr9:94903400-94903800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
49	chr9:94903400-94903800	Active TSS	Right Ventricle	heart
50	chr9:94903400-94903800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links