Variant report

Variant	rs4333675
Chromosome Location	chr9:95861276-95861277
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	TCF12	chr9:95860654-95861357	ECC-1	luminal epithelium:	n/a	chr9:95860686-95860694 chr9:95861096-95861106 chr9:95861024-95861031
2	TCF12	chr9:95860634-95861365	SK-N-SH	brain:	n/a	chr9:95860686-95860694 chr9:95861096-95861106 chr9:95861024-95861031
3	STAT3	chr9:95860818-95861337	MCF10A-Er-Src	breast:	n/a	chr9:95861045-95861054
4	FOSL2	chr9:95860700-95861381	SK-N-SH	brain:	n/a	chr9:95861043-95861054 chr9:95861044-95861056 chr9:95861028-95861039 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054
5	POLR2A	chr9:95860490-95861356	U87	brain:	n/a	n/a
6	GATA3	chr9:95860640-95861337	SK-N-SH	brain:	n/a	chr9:95861027-95861034 chr9:95860709-95860725 chr9:95860711-95860723 chr9:95860712-95860722 chr9:95860712-95860721
7	MYC	chr9:95860884-95861366	MCF10A-Er-Src	breast:	n/a	chr9:95861046-95861055
8	JUND	chr9:95860636-95861394	SK-N-SH	brain:	n/a	chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861044-95861055 chr9:95861029-95861037 chr9:95861045-95861054
9	PBX3	chr9:95860662-95861320	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr9:95860670-95861282	U87	brain:	n/a	n/a
11	NFIC	chr9:95860698-95861360	ECC-1	luminal epithelium:	n/a	n/a
12	JUN	chr9:95860734-95861398	K562	blood:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054
13	SP1	chr9:95860730-95861341	A549	lung:	n/a	n/a
14	FOS	chr9:95860832-95861342	MCF10A-Er-Src	breast:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038
15	NFIC	chr9:95860644-95861399	SK-N-SH	brain:	n/a	n/a
16	STAT3	chr9:95861085-95861514	MCF10A-Er-Src	breast:	n/a	n/a
17	FOSL2	chr9:95860742-95861298	HepG2	liver:	n/a	chr9:95861043-95861054 chr9:95861044-95861056 chr9:95861028-95861039 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054
18	POLR2A	chr9:95860711-95861355	HL-60	blood:	n/a	n/a
19	NFIC	chr9:95860729-95861355	ECC-1	luminal epithelium:	n/a	n/a
20	FOSL2	chr9:95860603-95861343	A549	lung:	n/a	chr9:95861043-95861054 chr9:95861044-95861056 chr9:95861028-95861039 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054
21	FOS	chr9:95860858-95861377	MCF10A-Er-Src	breast:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038
22	JUND	chr9:95860619-95861408	SK-N-SH	brain:	n/a	chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861044-95861055 chr9:95861029-95861037 chr9:95861045-95861054
23	MAZ	chr9:95860561-95861369	IMR90	lung:	n/a	chr9:95861046-95861055
24	POLR2A	chr9:95860702-95861303	HUVEC	blood vessel:	n/a	n/a
25	JUND	chr9:95860685-95861363	MCF-7	breast:	n/a	chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861044-95861055 chr9:95861029-95861037 chr9:95861045-95861054
26	MYC	chr9:95860885-95861368	MCF10A-Er-Src	breast:	n/a	chr9:95861046-95861055
27	TCF12	chr9:95860598-95861343	A549	lung:	n/a	chr9:95860686-95860694 chr9:95861096-95861106 chr9:95861024-95861031
28	TCF12	chr9:95860625-95861443	SK-N-SH	brain:	n/a	chr9:95860686-95860694 chr9:95861096-95861106 chr9:95861024-95861031
29	CEBPB	chr9:95860842-95861333	IMR90	lung:	n/a	n/a
30	POLR2A	chr9:95860756-95861297	SK-N-SH	brain:	n/a	n/a
31	MXI1	chr9:95859931-95861394	IMR90	lung:	n/a	n/a
32	CHD1	chr9:95860423-95861345	IMR90	lung:	n/a	n/a
33	POLR2A	chr9:95860792-95861282	HUVEC	blood vessel:	n/a	n/a
34	FOS	chr9:95860823-95861507	MCF10A-Er-Src	breast:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038
35	POLR2A	chr9:95860723-95861333	HUVEC	blood vessel:	n/a	n/a
36	EP300	chr9:95860597-95861466	SK-N-SH	brain:	n/a	chr9:95861015-95861031
37	RCOR1	chr9:95860188-95862102	IMR90	lung:	n/a	n/a
38	JUND	chr9:95860604-95861413	HCT-116	colon:	n/a	chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861044-95861055 chr9:95861029-95861037 chr9:95861045-95861054
39	JUND	chr9:95860718-95861378	SK-N-SH	brain:	n/a	chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861044-95861055 chr9:95861029-95861037 chr9:95861045-95861054
40	RXRA	chr9:95860677-95861375	SK-N-SH	brain:	n/a	n/a
41	TCF12	chr9:95860779-95861322	ECC-1	luminal epithelium:	n/a	chr9:95861096-95861106 chr9:95861024-95861031
42	FOSL1	chr9:95860582-95861388	HCT-116	colon:	n/a	chr9:95861044-95861055 chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054
43	MAX	chr9:95860624-95861384	A549	lung:	n/a	chr9:95861046-95861055
44	STAT3	chr9:95860976-95861360	MCF10A-Er-Src	breast:	n/a	chr9:95861045-95861054
45	FOSL1	chr9:95860427-95861400	HCT-116	colon:	n/a	chr9:95861044-95861055 chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054
46	FOS	chr9:95860769-95861318	HUVEC	blood vessel:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038
47	JUND	chr9:95860616-95861386	HCT-116	colon:	n/a	chr9:95861027-95861038 chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861044-95861055 chr9:95861029-95861037 chr9:95861045-95861054
48	FOS	chr9:95860851-95861493	MCF10A-Er-Src	breast:	n/a	chr9:95861044-95861056 chr9:95861045-95861055 chr9:95861027-95861039 chr9:95861029-95861037 chr9:95861045-95861054 chr9:95861044-95861055 chr9:95861027-95861038
49	CEBPB	chr9:95860929-95861345	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr9:95860484-95861335	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
2	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:
3	chr9:95857571..95862229-chr9:96211597..96216359,5	K562	blood:
4	chr9:95810158..95812137-chr9:95860234..95862505,2	K562	blood:
5	chr9:95816364..95826268-chr9:95852309..95863275,20	MCF-7	breast:
6	chr9:95765841..95768225-chr9:95860926..95862448,2	MCF-7	breast:
7	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
8	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
9	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223446	TF binding region
ENSG00000188938	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000157303	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10739942	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761193	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821067	0.95[ASN][1000 genomes]
rs10821070	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821071	0.94[ASN][1000 genomes]
rs1123000	0.95[ASN][1000 genomes]
rs1539672	0.95[ASN][1000 genomes]
rs2027585	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275849	0.82[AFR][1000 genomes]
rs2298242	0.95[ASN][1000 genomes]
rs2298243	0.95[ASN][1000 genomes]
rs3819011	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077822	0.98[ASN][1000 genomes]
rs4237219	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4384040	0.97[ASN][1000 genomes]
rs4743882	0.98[ASN][1000 genomes]
rs4743883	0.98[ASN][1000 genomes]
rs4743884	0.98[ASN][1000 genomes]
rs4743885	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743887	0.95[ASN][1000 genomes]
rs4744171	0.98[ASN][1000 genomes]
rs4744172	0.98[ASN][1000 genomes]
rs4744174	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744175	0.98[ASN][1000 genomes]
rs4744176	0.97[ASN][1000 genomes]
rs55902006	0.86[AFR][1000 genomes]
rs58767769	0.82[AFR][1000 genomes]
rs7020130	0.98[ASN][1000 genomes]
rs7028778	0.85[AFR][1000 genomes]
rs7031053	0.85[AFR][1000 genomes]
rs7857595	0.98[ASN][1000 genomes]
rs7868952	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4333675	C9orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95858800-95861800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:95859000-95861400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:95859000-95861800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr9:95859000-95862000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:95859200-95861800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr9:95859200-95861800	Enhancers	K562	blood
9	chr9:95859400-95862200	Enhancers	Pancreas	Pancrea
10	chr9:95859400-95862200	Enhancers	Spleen	Spleen
11	chr9:95859400-95862400	Enhancers	Primary B cells from peripheral blood	blood
12	chr9:95859400-95876200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:95859600-95861400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:95859600-95861600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:95859600-95861800	Enhancers	Liver	Liver
16	chr9:95859600-95861800	Enhancers	Lung	lung
17	chr9:95859600-95861800	Enhancers	Small Intestine	intestine
18	chr9:95859600-95862000	Enhancers	Fetal Lung	lung
19	chr9:95859600-95862200	Enhancers	Gastric	stomach
20	chr9:95859600-95862200	Enhancers	Right Atrium	heart
21	chr9:95859600-95862400	Enhancers	Placenta	Placenta
22	chr9:95859600-95862600	Enhancers	Ovary	ovary
23	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
24	chr9:95859800-95862000	Enhancers	Stomach Mucosa	stomach
25	chr9:95859800-95862200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:95859800-95862200	Enhancers	Fetal Muscle Leg	muscle
27	chr9:95859800-95862400	Enhancers	Left Ventricle	heart
28	chr9:95859800-95862600	Enhancers	Esophagus	oesophagus
29	chr9:95860000-95862800	Enhancers	Fetal Thymus	thymus
30	chr9:95860000-95863000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr9:95860200-95861600	Enhancers	Fetal Brain Male	brain
32	chr9:95860200-95862200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:95860200-95872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:95860400-95861800	Enhancers	Fetal Intestine Large	intestine
35	chr9:95860400-95861800	Enhancers	Fetal Muscle Trunk	muscle
36	chr9:95860400-95862400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:95860400-95862400	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr9:95860400-95863000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:95860400-95876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:95860600-95861600	Enhancers	Fetal Stomach	stomach
41	chr9:95860800-95863000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:95860800-95863000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr9:95860800-95872800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr9:95861000-95861400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:95861000-95861400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr9:95861000-95861400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr9:95861000-95861400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:95861000-95861400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:95861000-95861400	Enhancers	Adipose Nuclei	Adipose
50	chr9:95861000-95861400	Enhancers	Rectal Smooth Muscle	rectum

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