Variant report

Variant	rs532487845
Chromosome Location	chr9:95856939-95856940
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	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	PML	chr9:95856855-95858128	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:95856924-95858075	HepG2	liver:	n/a	n/a
6	RCOR1	chr9:95856792-95858032	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:95856565-95858072	GM12892	blood:	n/a	n/a
8	POLR2A	chr9:95856591-95859009	GM15510	blood:	n/a	n/a
9	ELF1	chr9:95856866-95858534	GM12878	blood:	n/a	chr9:95858163-95858175 chr9:95857211-95857224
10	EBF1	chr9:95856818-95857306	GM12878	blood:	n/a	n/a
11	NFIC	chr9:95856694-95857936	GM12878	blood:	n/a	n/a
12	MTA3	chr9:95856418-95857806	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:95856431-95858781	GM19099	blood:	n/a	n/a
14	POLR2A	chr9:95856779-95858067	SK-N-MC	brain:	n/a	n/a
15	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
16	BCLAF1	chr9:95856898-95857416	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:95856924-95858006	K562	blood:	n/a	n/a
18	STAT5A	chr9:95856828-95857805	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
19	RUNX3	chr9:95856666-95858017	GM12878	blood:	n/a	n/a
20	HEY1	chr9:95856703-95858011	K562	blood:	n/a	chr9:95857950-95857965
21	SPI1	chr9:95856846-95857553	HL-60	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
22	SPI1	chr9:95856582-95857640	GM12878	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
23	POLR2A	chr9:95856809-95856954	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr9:95856640-95858120	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:95856848-95858059	HL-60	blood:	n/a	n/a
26	POLR2A	chr9:95855594-95858126	GM19193	blood:	n/a	n/a
27	POLR2A	chr9:95856906-95858006	GM12891	blood:	n/a	n/a
28	POLR2A	chr9:95856579-95858093	K562	blood:	n/a	n/a
29	CHD1	chr9:95856862-95857801	GM12878	blood:	n/a	n/a
30	CREB1	chr9:95856893-95858595	GM12878	blood:	n/a	n/a
31	STAT5A	chr9:95856802-95857898	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
32	POLR2A	chr9:95856866-95858088	GM12891	blood:	n/a	n/a
33	NFIC	chr9:95856883-95857853	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:95856574-95858883	GM18951	blood:	n/a	n/a
35	POLR2A	chr9:95856556-95859175	GM18505	blood:	n/a	n/a
36	POLR2A	chr9:95856655-95858119	GM18526	blood:	n/a	n/a
37	POLR2A	chr9:95856843-95858029	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:95856878-95857222	HCT-116	colon:	n/a	n/a
39	CHD2	chr9:95856939-95858098	GM12878	blood:	n/a	n/a
40	POU2F2	chr9:95856911-95857864	GM12878	blood:	n/a	chr9:95857480-95857492 chr9:95857821-95857833
41	NFATC1	chr9:95856934-95857491	GM12878	blood:	n/a	n/a
42	POLR2A	chr9:95856508-95858092	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:95856595-95858170	GM12892	blood:	n/a	n/a
44	MTA3	chr9:95855540-95858006	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:95855591-95858135	GM12878	blood:	n/a	n/a
46	SPI1	chr9:95856926-95857428	GM12891	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
47	PAX5	chr9:95856875-95857766	GM12878	blood:	n/a	n/a
48	POLR2A	chr9:95855539-95858018	GM12891	blood:	n/a	n/a
49	SPI1	chr9:95856903-95857380	GM12878	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
50	YY1	chr9:95856919-95858139	GM12892	blood:	n/a	n/a

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	chr9:95856800..95859803-chr9:96212504..96215667,3	MCF-7	breast:
12	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
13	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
14	chr20:52231451..52233410-chr9:95855807..95857476,2	MCF-7	breast:
15	chr9:95818697..95822651-chr9:95855885..95860349,6	MCF-7	breast:
16	chr9:95855374..95857011-chr9:96211842..96214565,2	K562	blood:
17	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NINJ1-1	chr9:95856723-95857296	NONHSAT133232

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:102 , 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	chr9:95840400-95857000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:95845200-95857200	Weak transcription	Small Intestine	intestine
4	chr9:95846400-95857000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:95848600-95857000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:95849400-95857400	Weak transcription	Ovary	ovary
7	chr9:95853400-95857000	Enhancers	Primary B cells from cord blood	blood
8	chr9:95853400-95857200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr9:95853400-95857200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr9:95853600-95857200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr9:95853800-95857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:95854000-95857000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:95854000-95857200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr9:95854000-95857200	Enhancers	Spleen	Spleen
15	chr9:95854000-95857400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:95854000-95857400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:95854200-95857000	Weak transcription	A549	lung
18	chr9:95854200-95857200	Weak transcription	Gastric	stomach
19	chr9:95854400-95857200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr9:95854400-95857400	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:95854400-95857400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:95854400-95857400	Enhancers	Fetal Muscle Trunk	muscle
23	chr9:95854400-95857400	Enhancers	Fetal Muscle Leg	muscle
24	chr9:95854400-95857400	Enhancers	Placenta	Placenta
25	chr9:95854600-95857000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:95854600-95857200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:95854600-95857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:95854600-95857200	Enhancers	Adipose Nuclei	Adipose
29	chr9:95854600-95857400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:95854600-95857400	Enhancers	Fetal Thymus	thymus
31	chr9:95854600-95857400	Weak transcription	NHDF-Ad	bronchial
32	chr9:95854600-95857800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr9:95854800-95857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:95854800-95857000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr9:95854800-95857200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr9:95854800-95857200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:95854800-95857200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr9:95854800-95857200	Weak transcription	HMEC	breast
39	chr9:95854800-95857400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr9:95854800-95857400	Enhancers	Fetal Intestine Large	intestine
41	chr9:95854800-95857400	Weak transcription	NH-A	brain
42	chr9:95854800-95857800	Enhancers	Fetal Heart	heart
43	chr9:95855000-95857000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr9:95855000-95857000	Enhancers	Colonic Mucosa	Colon
45	chr9:95855000-95857200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:95855000-95857200	Enhancers	Duodenum Mucosa	Duodenum
47	chr9:95855000-95857400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr9:95855000-95857400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr9:95855000-95857400	Enhancers	Fetal Lung	lung
50	chr9:95855000-95857400	Enhancers	Fetal Stomach	stomach

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