Variant report

Variant	rs13288200
Chromosome Location	chr9:95857333-95857334
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	chr9:95856759-95858016	GM12892	blood:	n/a	n/a
2	POLR2A	chr9:95856331-95857908	K562	blood:	n/a	n/a
3	POLR2A	chr9:95856452-95858145	GM12892	blood:	n/a	n/a
4	TAF1	chr9:95857296-95858044	ECC-1	luminal epithelium:	n/a	n/a
5	PML	chr9:95856855-95858128	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:95857084-95857972	K562	blood:	n/a	n/a
7	POLR2A	chr9:95857294-95858042	MCF10A-Er-Src	breast:	n/a	n/a
8	ELF1	chr9:95857071-95857341	HepG2	liver:	n/a	chr9:95857211-95857224
9	POLR2A	chr9:95856924-95858075	HepG2	liver:	n/a	n/a
10	EP300	chr9:95856989-95858019	GM12878	blood:	n/a	chr9:95857125-95857141
11	RCOR1	chr9:95856792-95858032	GM12878	blood:	n/a	n/a
12	MAZ	chr9:95856950-95859166	GM12878	blood:	n/a	chr9:95857476-95857486 chr9:95858208-95858218 chr9:95858272-95858282 chr9:95858894-95858904
13	ELK1	chr9:95857012-95858255	GM12878	blood:	n/a	n/a
14	WRNIP1	chr9:95857195-95857395	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:95856565-95858072	GM12892	blood:	n/a	n/a
16	SMC3	chr9:95857027-95857732	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:95856591-95859009	GM15510	blood:	n/a	n/a
18	ELF1	chr9:95856866-95858534	GM12878	blood:	n/a	chr9:95858163-95858175 chr9:95857211-95857224
19	ZEB1	chr9:95857328-95858044	GM12878	blood:	n/a	n/a
20	HEY1	chr9:95857163-95857363	K562	blood:	n/a	n/a
21	MAX	chr9:95857059-95858054	GM12878	blood:	n/a	chr9:95857476-95857486
22	POLR2A	chr9:95857019-95858057	HepG2	liver:	n/a	n/a
23	NFIC	chr9:95856694-95857936	GM12878	blood:	n/a	n/a
24	POU2F2	chr9:95857121-95857361	GM12878	blood:	n/a	n/a
25	TBP	chr9:95857017-95858664	K562	blood:	n/a	n/a
26	MTA3	chr9:95856418-95857806	GM12878	blood:	n/a	n/a
27	POLR2A	chr9:95856431-95858781	GM19099	blood:	n/a	n/a
28	CREB1	chr9:95857183-95859262	HepG2	liver:	n/a	n/a
29	POLR2A	chr9:95856779-95858067	SK-N-MC	brain:	n/a	n/a
30	ESRRA	chr9:95856588-95859429	GM12878	blood:	n/a	chr9:95858752-95858764 chr9:95858752-95858762 chr9:95859336-95859355 chr9:95858748-95858764 chr9:95858744-95858763 chr9:95857976-95857989 chr9:95856813-95856827
31	BCLAF1	chr9:95856898-95857416	GM12878	blood:	n/a	n/a
32	POLR2A	chr9:95856924-95858006	K562	blood:	n/a	n/a
33	MYC	chr9:95857042-95858160	NB4	blood:	n/a	chr9:95857476-95857486
34	STAT5A	chr9:95856828-95857805	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
35	RUNX3	chr9:95856666-95858017	GM12878	blood:	n/a	n/a
36	HEY1	chr9:95856703-95858011	K562	blood:	n/a	chr9:95857950-95857965
37	SPI1	chr9:95856846-95857553	HL-60	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
38	SPI1	chr9:95856582-95857640	GM12878	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
39	BHLHE40	chr9:95857060-95858089	K562	blood:	n/a	chr9:95857165-95857181
40	POLR2A	chr9:95856640-95858120	GM12878	blood:	n/a	n/a
41	STAT3	chr9:95857031-95857697	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
42	POLR2A	chr9:95856848-95858059	HL-60	blood:	n/a	n/a
43	POLR2A	chr9:95855594-95858126	GM19193	blood:	n/a	n/a
44	POLR2A	chr9:95856906-95858006	GM12891	blood:	n/a	n/a
45	TEAD4	chr9:95857085-95857393	H1-hESC	embryonic stem cell:	n/a	n/a
46	BCLAF1	chr9:95857012-95858021	GM12878	blood:	n/a	chr9:95857949-95857962
47	POLR2A	chr9:95856579-95858093	K562	blood:	n/a	n/a
48	CHD1	chr9:95856862-95857801	GM12878	blood:	n/a	n/a
49	CREB1	chr9:95856893-95858595	GM12878	blood:	n/a	n/a
50	STAT5A	chr9:95856802-95857898	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163

No.	Distal block	Cell Line	Cell type
1	chr9:95832455..95836206-chr9:95854622..95857563,3	K562	blood:
2	chr9:95819533..95824260-chr9:95855982..95859349,6	K562	blood:
3	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
4	chr9:95782411..95784335-chr9:95855706..95857608,2	K562	blood:
5	chr9:95856307..95858930-chr9:95945344..95947454,2	MCF-7	breast:
6	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:
7	chr9:95644477..95647026-chr9:95856409..95858869,2	MCF-7	breast:
8	chr9:95856094..95858375-chr9:96337008..96340445,3	MCF-7	breast:
9	chr9:95819521..95827100-chr9:95855273..95859349,14	K562	blood:
10	chr9:95816364..95826268-chr9:95852309..95863275,20	MCF-7	breast:
11	chr9:95856977..95859126-chr9:95888088..95890598,2	MCF-7	breast:
12	chr9:95856800..95859803-chr9:96212504..96215667,3	MCF-7	breast:
13	chr9:95857275..95859572-chr9:95888374..95892185,3	MCF-7	breast:
14	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
15	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
16	chr20:52231451..52233410-chr9:95855807..95857476,2	MCF-7	breast:
17	chr9:95818697..95822651-chr9:95855885..95860349,6	MCF-7	breast:
18	chr22:39715499..39716297-chr9:95857044..95857925,2	Hela-S3	cervix:
19	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:

Variant related genes	Relation type
C9orf89	TF binding region
ENSG00000165238	Chromatin interaction
ENSG00000226668	Chromatin interaction
ENSG00000157303	Chromatin interaction
ENSG00000100316	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000197724	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12003264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs13286624	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs17593496	0.88[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs62573574	0.82[EUR][1000 genomes]
rs7025686	0.87[YRI][hapmap]

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	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
10	esv3438320	chr9:95856656-95859504	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	esv3346305	chr9:95857306-95859804	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13288200	NINJ1	Cis_1M	lymphoblastoid	RTeQTL
rs13288200	NINJ1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95834400-95857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95849400-95857400	Weak transcription	Ovary	ovary
3	chr9:95854000-95857400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:95854000-95857400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:95854400-95857400	Enhancers	Primary hematopoietic stem cells	blood
6	chr9:95854400-95857400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:95854400-95857400	Enhancers	Fetal Muscle Trunk	muscle
8	chr9:95854400-95857400	Enhancers	Fetal Muscle Leg	muscle
9	chr9:95854400-95857400	Enhancers	Placenta	Placenta
10	chr9:95854600-95857400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:95854600-95857400	Enhancers	Fetal Thymus	thymus
12	chr9:95854600-95857400	Weak transcription	NHDF-Ad	bronchial
13	chr9:95854600-95857800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr9:95854800-95857400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:95854800-95857400	Enhancers	Fetal Intestine Large	intestine
16	chr9:95854800-95857400	Weak transcription	NH-A	brain
17	chr9:95854800-95857800	Enhancers	Fetal Heart	heart
18	chr9:95855000-95857400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr9:95855000-95857400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr9:95855000-95857400	Enhancers	Fetal Lung	lung
21	chr9:95855000-95857400	Enhancers	Fetal Stomach	stomach
22	chr9:95855000-95857400	Enhancers	Lung	lung
23	chr9:95855000-95857400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr9:95855000-95857400	Enhancers	Right Atrium	heart
25	chr9:95855000-95857400	Weak transcription	Osteobl	bone
26	chr9:95855200-95857400	Enhancers	Fetal Intestine Small	intestine
27	chr9:95855200-95857800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr9:95855400-95857400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr9:95855400-95857400	Enhancers	Stomach Mucosa	stomach
30	chr9:95855400-95857800	Flanking Active TSS	GM12878-XiMat	blood
31	chr9:95855600-95857400	Enhancers	Brain Anterior Caudate	brain
32	chr9:95855600-95857800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:95856000-95857400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:95856000-95857400	Enhancers	Esophagus	oesophagus
35	chr9:95856000-95857400	Enhancers	Left Ventricle	heart
36	chr9:95856000-95857400	Enhancers	Right Ventricle	heart
37	chr9:95856200-95857400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:95856200-95857400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:95856200-95857400	Weak transcription	Fetal Brain Female	brain
40	chr9:95856400-95857400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:95856400-95857400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:95856400-95857400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:95856600-95857400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:95856600-95857400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:95856600-95857400	Weak transcription	Brain Substantia Nigra	brain
46	chr9:95856800-95857400	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:95856800-95857400	Enhancers	Colon Smooth Muscle	Colon
48	chr9:95856800-95857400	Flanking Active TSS	HepG2	liver
49	chr9:95856800-95857800	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr9:95857000-95857400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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