Variant report

Variant	rs556897967
Chromosome Location	chr9:14346861-14346862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr9:14346816-14350234	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:14346137-14347762	H1-neurons	neurons:	n/a	n/a
3	SUZ12	chr9:14344009-14351112	NT2-D1	testis:	n/a	n/a
4	POLR2A	chr9:14346746-14347111	H1-hESC	embryonic stem cell:	n/a	n/a
5	NANOG	chr9:14346861-14347081	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr9:14345434-14350297	H1-hESC	embryonic stem cell:	n/a	chr9:14347438-14347447 chr9:14348586-14348595 chr9:14347099-14347108 chr9:14348579-14348592
7	E2F6	chr9:14345336-14349202	H1-hESC	embryonic stem cell:	n/a	chr9:14348935-14348947 chr9:14347246-14347258
8	CHD2	chr9:14346836-14348140	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr9:14344897-14346945	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:14344417-14347484	H1-neurons	neurons:	n/a	n/a
11	MYC	chr9:14346163-14347052	H1-hESC	embryonic stem cell:	n/a	chr9:14346375-14346384
12	POLR2A	chr9:14344732-14347104	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:14346834-14346884	AG04450	lung:	fetal
2	chr9:14346834-14346884	Jurkat	blood:	n/a
3	chr9:14346834-14346884	GM12892	blood:	n/a
4	chr9:14346834-14346884	GM12891	blood:	n/a
5	chr9:14346834-14346884	ECC-1	luminal epithelium:	n/a
6	chr9:14346834-14346884	BJ	skin:	n/a
7	chr9:14346834-14346884	HL-60	blood:	n/a
8	chr9:14346834-14346884	HRCEpiC	kidney:	n/a
9	chr9:14346834-14346884	HNPCEpiC	eye:	n/a
10	chr9:14346834-14346884	HMEC	breast:	n/a
11	chr9:14346834-14346884	SK-N-MC	brain:	n/a
12	chr9:14346834-14346884	Caco-2	colon:	n/a
13	chr9:14346834-14346884	MCF-7	breast:	n/a
14	chr9:14346834-14346884	A549	lung:	n/a
15	chr9:14346834-14346884	HCT-116	colon:	n/a
16	chr9:14346834-14346884	AG09309	skin:	n/a
17	chr9:14346834-14346884	ovcar-3	ovarian:	n/a
18	chr9:14346834-14346884	BE2_C	brain:	n/a
19	chr9:14346834-14346884	PFSK-1	brain:	n/a
20	chr9:14346834-14346884	AG04449	skin:	fetal
21	chr9:14346834-14346884	HRPEpiC	eye:	n/a
22	chr9:14346834-14346884	NH-A	brain:	n/a
23	chr9:14346834-14346884	HCF	heart:	n/a
24	chr9:14346834-14346884	SKMC	muscle:	n/a
25	chr9:14346834-14346884	RPTEC	kidney:	n/a
26	chr9:14346834-14346884	HRE	kidney:	n/a
27	chr9:14346834-14346884	HEK293	kidney:	embryo
28	chr9:14346834-14346884	AG10803	skin:	n/a
29	chr9:14346834-14346884	PrEC	prostate:	n/a
30	chr9:14346834-14346884	HCPEpiC	choroid plexus:	n/a
31	chr9:14346834-14346884	U87	brain:	n/a
32	chr9:14346834-14346884	SK-N-SH_RA	brain:	n/a
33	chr9:14346834-14346884	AG09319	gingival:	n/a
34	chr9:14346834-14346884	PANC-1	pancreas:	n/a
35	chr9:14346834-14346884	GM19239	blood:	n/a
36	chr9:14346834-14346884	NT2-D1	testis:	n/a
37	chr9:14346834-14346884	ProgFib	skin:	n/a
38	chr9:14346834-14346884	NHDF-neo	bronchial:	n/a
39	chr9:14346834-14346884	HUVEC	blood vessel:	n/a
40	chr9:14346834-14346884	HAEpiC	amniotic membrane:	n/a
41	chr9:14346834-14346884	Hela-S3	cervix:	n/a
42	chr9:14346834-14346884	GM06990	blood:	n/a
43	chr9:14346834-14346884	HEEpiC	esophagus:	n/a
44	chr9:14346834-14346884	GM12878	blood:	n/a
45	chr9:14346834-14346884	SK-N-SH	brain:	n/a
46	chr9:14346834-14346884	HIPEpiC	eye:	n/a
47	chr9:14346834-14346884	CMK	blood:	n/a
48	chr9:14346834-14346884	SAEC	small airway:	n/a
49	chr9:14346834-14346884	T-47D	breast:	n/a
50	chr9:14346834-14346884	LNCaP	prostate:	n/a

No data

Variant related genes	Relation type
ENSG00000225472	TF binding region
ENSG00000225472	CpG island

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv916811	chr9:14210978-14542068	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv831516	chr9:14280695-14437445	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv892599	chr9:14310504-14350469	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv523410	chr9:14344888-14348563	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv527980	chr9:14345605-14348563	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14343800-14350800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr9:14343800-14351000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:14344000-14348600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:14344000-14349200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr9:14344200-14348200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr9:14344600-14347200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr9:14344600-14350800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr9:14345000-14347000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:14345000-14347000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
10	chr9:14345000-14349000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:14345000-14349000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr9:14345200-14347200	Weak transcription	A549	lung
13	chr9:14345400-14347000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:14345400-14347800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
15	chr9:14345400-14350000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:14345600-14347600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:14345600-14347600	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr9:14345600-14347800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:14345600-14347800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
20	chr9:14345600-14349000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr9:14345600-14351000	Active TSS	Right Atrium	heart
22	chr9:14345800-14347000	Enhancers	Lung	lung
23	chr9:14345800-14347200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr9:14345800-14347400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
25	chr9:14345800-14347600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
26	chr9:14345800-14347800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
27	chr9:14345800-14348000	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr9:14345800-14348200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:14345800-14349000	Bivalent Enhancer	Fetal Thymus	thymus
30	chr9:14345800-14350000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
31	chr9:14345800-14350200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr9:14346000-14347200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:14346000-14347400	Enhancers	Gastric	stomach
34	chr9:14346000-14348200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr9:14346000-14348200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr9:14346000-14348400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:14346000-14349000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr9:14346000-14350000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr9:14346200-14348000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:14346200-14350400	Active TSS	Brain Substantia Nigra	brain
41	chr9:14346200-14350800	Active TSS	Brain Hippocampus Middle	brain
42	chr9:14346400-14347000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:14346400-14347200	Flanking Active TSS	Right Ventricle	heart
44	chr9:14346400-14347400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:14346400-14347400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:14346400-14347800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
47	chr9:14346400-14348400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
48	chr9:14346400-14349400	Active TSS	Esophagus	oesophagus
49	chr9:14346600-14347000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:14346600-14347000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links