Variant report

Variant	rs45488691
Chromosome Location	chr9:104295643-104295644
allele	C/T
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	SP1	chr9:104295556-104296266	GM12878	blood:	n/a	chr9:104296121-104296130 chr9:104296120-104296132 chr9:104296120-104296132 chr9:104296122-104296131 chr9:104296121-104296135
2	POLR2A	chr9:104295641-104296507	MCF-7	breast:	n/a	n/a
3	PBX3	chr9:104295419-104296455	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:104295638-104296589	Hela-S3	cervix:	n/a	n/a
5	FOS	chr9:104295625-104295766	MCF10A-Er-Src	breast:	n/a	n/a
6	TBL1XR1	chr9:104295387-104296369	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:104295579-104296494	HepG2	liver:	n/a	n/a
8	GTF2F1	chr9:104295621-104296746	Hela-S3	cervix:	n/a	n/a
9	PBX3	chr9:104295585-104296052	A549	lung:	n/a	n/a
10	MAX	chr9:104295618-104296583	SK-N-SH	brain:	n/a	n/a
11	EP300	chr9:104295617-104296272	HepG2	liver:	n/a	chr9:104296087-104296096 chr9:104296131-104296138 chr9:104296094-104296108
12	GABPA	chr9:104295442-104296711	SK-N-SH	brain:	n/a	chr9:104295974-104295988
13	TCF12	chr9:104295512-104296612	A549	lung:	n/a	n/a
14	WRNIP1	chr9:104295494-104296768	GM12878	blood:	n/a	n/a
15	MYC	chr9:104295345-104296561	K562	blood:	n/a	n/a
16	MYC	chr9:104295400-104296537	K562	blood:	n/a	n/a
17	CREB1	chr9:104295587-104296315	K562	blood:	n/a	n/a
18	SP2	chr9:104295493-104296293	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:104295407-104296609	H1-hESC	embryonic stem cell:	n/a	n/a
20	CREB1	chr9:104295530-104296403	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:104295572-104296630	Hela-S3	cervix:	n/a	n/a
22	CHD2	chr9:104295631-104296545	K562	blood:	n/a	n/a
23	POLR2A	chr9:104295522-104296459	MCF10A-Er-Src	breast:	n/a	n/a
24	TBP	chr9:104295617-104296395	H1-hESC	embryonic stem cell:	n/a	n/a
25	REST	chr9:104295267-104296803	H1-neurons	neurons:	n/a	chr9:104296111-104296124
26	PBX3	chr9:104295384-104296380	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr9:104295445-104296794	GM19099	blood:	n/a	n/a
28	TBP	chr9:104295475-104296597	Hela-S3	cervix:	n/a	n/a
29	STAT3	chr9:104295621-104296258	MCF10A-Er-Src	breast:	n/a	chr9:104295668-104295676
30	ELF1	chr9:104295552-104296538	HCT-116	colon:	n/a	chr9:104296128-104296139 chr9:104296129-104296138
31	GABPA	chr9:104295582-104296685	SK-N-SH	brain:	n/a	chr9:104295974-104295988
32	NR2F2	chr9:104295478-104296591	K562	blood:	n/a	chr9:104295879-104295894 chr9:104296155-104296170
33	POLR2A	chr9:104295518-104296650	K562	blood:	n/a	n/a
34	CBX3	chr9:104295495-104296375	K562	blood:	n/a	n/a
35	NFYB	chr9:104295544-104296173	Hela-S3	cervix:	n/a	chr9:104295783-104295798
36	ELF1	chr9:104295606-104296414	HepG2	liver:	n/a	chr9:104296128-104296139 chr9:104296129-104296138
37	PBX3	chr9:104295577-104296093	A549	lung:	n/a	n/a
38	MAX	chr9:104295517-104296309	H1-hESC	embryonic stem cell:	n/a	n/a
39	SP1	chr9:104295415-104296477	A549	lung:	n/a	chr9:104296121-104296130 chr9:104296120-104296132 chr9:104296120-104296132 chr9:104296122-104296131 chr9:104296121-104296135
40	CEBPB	chr9:104295635-104296201	A549	lung:	n/a	n/a
41	POLR2A	chr9:104295331-104296644	U87	brain:	n/a	n/a
42	ELF1	chr9:104295534-104296622	MCF-7	breast:	n/a	chr9:104296128-104296139 chr9:104296129-104296138
43	NFYA	chr9:104295540-104296243	K562	blood:	n/a	chr9:104295786-104295804
44	MAX	chr9:104295505-104296463	ECC-1	luminal epithelium:	n/a	n/a
45	SP1	chr9:104295440-104296470	A549	lung:	n/a	chr9:104296121-104296130 chr9:104296120-104296132 chr9:104296120-104296132 chr9:104296122-104296131 chr9:104296121-104296135
46	MAX	chr9:104295502-104296263	GM12878	blood:	n/a	n/a
47	POLR2A	chr9:104295604-104296365	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr9:104295524-104296837	GM12878	blood:	n/a	n/a
49	SIX5	chr9:104295606-104296380	A549	lung:	n/a	n/a
50	CREB1	chr9:104295589-104296560	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:104295632-104295682	HIPEpiC	eye:	n/a
2	chr9:104295632-104295682	HRE	kidney:	n/a
3	chr9:104295632-104295682	HRCEpiC	kidney:	n/a
4	chr9:104295632-104295682	HL-60	blood:	n/a
5	chr9:104295632-104295682	BE2_C	brain:	n/a
6	chr9:104295632-104295682	HCF	heart:	n/a
7	chr9:104295632-104295682	SK-N-SH_RA	brain:	n/a
8	chr9:104295632-104295682	HAEpiC	amniotic membrane:	n/a
9	chr9:104295632-104295682	GM12892	blood:	n/a
10	chr9:104295632-104295682	SAEC	small airway:	n/a
11	chr9:104295632-104295682	PrEC	prostate:	n/a
12	chr9:104295632-104295682	NT2-D1	testis:	n/a
13	chr9:104295632-104295682	NHDF-neo	bronchial:	n/a
14	chr9:104295632-104295682	HPAEpiC	pulmonary alveolar:	n/a
15	chr9:104295632-104295682	U87	brain:	n/a
16	chr9:104295632-104295682	GM06990	blood:	n/a
17	chr9:104295632-104295682	PANC-1	pancreas:	n/a
18	chr9:104295632-104295682	LNCaP	prostate:	n/a
19	chr9:104295632-104295682	RPTEC	kidney:	n/a
20	chr9:104295632-104295682	H1-hESC	embryonic stem cell:	embryo
21	chr9:104295632-104295682	Hepatocyte	liver:	n/a
22	chr9:104295632-104295682	Hela-S3	cervix:	n/a
23	chr9:104295632-104295682	HUVEC	blood vessel:	n/a
24	chr9:104295632-104295682	A549	lung:	n/a
25	chr9:104295632-104295682	PFSK-1	brain:	n/a
26	chr9:104295632-104295682	HRPEpiC	eye:	n/a
27	chr9:104295632-104295682	CMK	blood:	n/a
28	chr9:104295632-104295682	HEK293	kidney:	embryo
29	chr9:104295632-104295682	AG04450	lung:	fetal
30	chr9:104295632-104295682	GM12891	blood:	n/a
31	chr9:104295632-104295682	MCF-7	breast:	n/a
32	chr9:104295632-104295682	IMR90	lung:	fetal
33	chr9:104295632-104295682	HNPCEpiC	eye:	n/a
34	chr9:104295632-104295682	HepG2	liver:	n/a
35	chr9:104295632-104295682	AG09309	skin:	n/a
36	chr9:104295632-104295682	SK-N-SH	brain:	n/a
37	chr9:104295632-104295682	NHBE	bronchial:	n/a
38	chr9:104295632-104295682	ProgFib	skin:	n/a
39	chr9:104295632-104295682	NH-A	brain:	n/a
40	chr9:104295632-104295682	AoSMC	blood vessel:	n/a
41	chr9:104295632-104295682	BJ	skin:	n/a
42	chr9:104295632-104295682	K562	blood:	n/a
43	chr9:104295632-104295682	ECC-1	luminal epithelium:	n/a
44	chr9:104295632-104295682	HCPEpiC	choroid plexus:	n/a
45	chr9:104295632-104295682	HCM	heart:	n/a
46	chr9:104295632-104295682	AG09319	gingival:	n/a
47	chr9:104295632-104295682	AG10803	skin:	n/a
48	chr9:104295632-104295682	GM12878	blood:	n/a
49	chr9:104295632-104295682	Jurkat	blood:	n/a
50	chr9:104295632-104295682	AG04449	skin:	fetal

Variant related genes	Relation type
RNF20	TF binding region
RNF20	CpG island

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10115763	0.85[ASN][1000 genomes]
rs10989553	0.85[ASN][1000 genomes]
rs12342026	0.89[ASN][1000 genomes]
rs12342991	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12343288	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12347518	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13284984	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13290720	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13295809	0.88[ASN][1000 genomes]
rs16920473	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1885977	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929496	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28533545	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34153995	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34727333	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36004060	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3739722	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3824473	0.89[ASN][1000 genomes]
rs3903804	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4119332	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59770438	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7030238	0.85[ASN][1000 genomes]
rs7034754	0.96[ASN][1000 genomes]
rs9299345	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104291600-104295800	Weak transcription	Small Intestine	intestine
2	chr9:104295000-104296200	Active TSS	Fetal Lung	lung
3	chr9:104295200-104295800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr9:104295200-104295800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:104295200-104295800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr9:104295200-104295800	Flanking Active TSS	Osteobl	bone
7	chr9:104295200-104296400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:104295200-104296600	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr9:104295200-104296800	Active TSS	Brain Substantia Nigra	brain
10	chr9:104295200-104296800	Active TSS	Colon Smooth Muscle	Colon
11	chr9:104295200-104297000	Active TSS	Fetal Brain Female	brain
12	chr9:104295200-104297200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr9:104295200-104297200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:104295200-104297200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr9:104295200-104297200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr9:104295200-104297200	Active TSS	Stomach Smooth Muscle	stomach
17	chr9:104295200-104297200	Active TSS	K562	blood
18	chr9:104295400-104295800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:104295400-104295800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:104295400-104295800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:104295400-104295800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:104295400-104295800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr9:104295400-104295800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr9:104295400-104295800	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr9:104295400-104295800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr9:104295400-104295800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr9:104295400-104295800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:104295400-104295800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:104295400-104295800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr9:104295400-104295800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:104295400-104295800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr9:104295400-104295800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:104295400-104295800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr9:104295400-104295800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:104295400-104295800	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr9:104295400-104295800	Flanking Active TSS	Liver	Liver
37	chr9:104295400-104295800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr9:104295400-104295800	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr9:104295400-104295800	Flanking Active TSS	Dnd41	blood
40	chr9:104295400-104295800	Flanking Active TSS	Hela-S3	cervix
41	chr9:104295400-104295800	Flanking Active TSS	HepG2	liver
42	chr9:104295400-104295800	Flanking Active TSS	HMEC	breast
43	chr9:104295400-104295800	Flanking Active TSS	HUVEC	blood vessel
44	chr9:104295400-104295800	Flanking Active TSS	NH-A	brain
45	chr9:104295400-104295800	Flanking Active TSS	NHLF	lung
46	chr9:104295400-104296000	Flanking Active TSS	Placenta	Placenta
47	chr9:104295400-104296200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:104295400-104296400	Active TSS	Brain Cingulate Gyrus	brain
49	chr9:104295400-104296400	Active TSS	Fetal Thymus	thymus
50	chr9:104295400-104296400	Active TSS	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links