Variant report

Variant	rs527553585
Chromosome Location	chr9:95857042-95857043
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	BCL11A	chr9:95857007-95857279	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:95856759-95858016	GM12892	blood:	n/a	n/a
3	POLR2A	chr9:95856331-95857908	K562	blood:	n/a	n/a
4	POLR2A	chr9:95856452-95858145	GM12892	blood:	n/a	n/a
5	PML	chr9:95856855-95858128	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:95856924-95858075	HepG2	liver:	n/a	n/a
7	EP300	chr9:95856989-95858019	GM12878	blood:	n/a	chr9:95857125-95857141
8	RCOR1	chr9:95856792-95858032	GM12878	blood:	n/a	n/a
9	MAZ	chr9:95856950-95859166	GM12878	blood:	n/a	chr9:95857476-95857486 chr9:95858208-95858218 chr9:95858272-95858282 chr9:95858894-95858904
10	ELK1	chr9:95857012-95858255	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:95856565-95858072	GM12892	blood:	n/a	n/a
12	SMC3	chr9:95857027-95857732	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:95856591-95859009	GM15510	blood:	n/a	n/a
14	TCF12	chr9:95857019-95857263	GM12878	blood:	n/a	n/a
15	ELF1	chr9:95856866-95858534	GM12878	blood:	n/a	chr9:95858163-95858175 chr9:95857211-95857224
16	EBF1	chr9:95856818-95857306	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:95857019-95858057	HepG2	liver:	n/a	n/a
18	NFIC	chr9:95856694-95857936	GM12878	blood:	n/a	n/a
19	TBP	chr9:95857017-95858664	K562	blood:	n/a	n/a
20	MTA3	chr9:95856418-95857806	GM12878	blood:	n/a	n/a
21	POLR2A	chr9:95856431-95858781	GM19099	blood:	n/a	n/a
22	POLR2A	chr9:95856779-95858067	SK-N-MC	brain:	n/a	n/a
23	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
24	BCLAF1	chr9:95856898-95857416	GM12878	blood:	n/a	n/a
25	POLR2A	chr9:95856924-95858006	K562	blood:	n/a	n/a
26	MYC	chr9:95857042-95858160	NB4	blood:	n/a	chr9:95857476-95857486
27	STAT5A	chr9:95856828-95857805	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
28	RUNX3	chr9:95856666-95858017	GM12878	blood:	n/a	n/a
29	HEY1	chr9:95856703-95858011	K562	blood:	n/a	chr9:95857950-95857965
30	SPI1	chr9:95856846-95857553	HL-60	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
31	SPI1	chr9:95856582-95857640	GM12878	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
32	SPI1	chr9:95857019-95857296	K562	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
33	POLR2A	chr9:95856640-95858120	GM12878	blood:	n/a	n/a
34	STAT3	chr9:95857031-95857697	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
35	POLR2A	chr9:95856848-95858059	HL-60	blood:	n/a	n/a
36	POLR2A	chr9:95855594-95858126	GM19193	blood:	n/a	n/a
37	SPI1	chr9:95857009-95857310	GM12878	blood:	n/a	chr9:95857149-95857156 chr9:95857145-95857158
38	POLR2A	chr9:95856906-95858006	GM12891	blood:	n/a	n/a
39	BCLAF1	chr9:95857012-95858021	GM12878	blood:	n/a	chr9:95857949-95857962
40	POLR2A	chr9:95856579-95858093	K562	blood:	n/a	n/a
41	CHD1	chr9:95856862-95857801	GM12878	blood:	n/a	n/a
42	CREB1	chr9:95856893-95858595	GM12878	blood:	n/a	n/a
43	STAT5A	chr9:95856802-95857898	GM12878	blood:	n/a	chr9:95857476-95857488 chr9:95857140-95857152 chr9:95857152-95857163
44	TAF1	chr9:95856999-95857386	GM12878	blood:	n/a	n/a
45	FOXM1	chr9:95856977-95858150	GM12878	blood:	n/a	n/a
46	POLR2A	chr9:95856866-95858088	GM12891	blood:	n/a	n/a
47	BHLHE40	chr9:95856998-95858083	GM12878	blood:	n/a	chr9:95857165-95857181
48	NFIC	chr9:95856883-95857853	GM12878	blood:	n/a	n/a
49	POLR2A	chr9:95856574-95858883	GM18951	blood:	n/a	n/a
50	RELA	chr9:95857019-95857830	GM18951	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	chr9:95856977..95859126-chr9:95888088..95890598,2	MCF-7	breast:
12	chr9:95856800..95859803-chr9:96212504..96215667,3	MCF-7	breast:
13	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
14	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
15	chr20:52231451..52233410-chr9:95855807..95857476,2	MCF-7	breast:
16	chr9:95818697..95822651-chr9:95855885..95860349,6	MCF-7	breast:
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
ENSG00000165238	Chromatin interaction
ENSG00000226668	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000197724	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000157303	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:107 , 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	chr9:95845200-95857200	Weak transcription	Small Intestine	intestine
3	chr9:95849400-95857400	Weak transcription	Ovary	ovary
4	chr9:95853400-95857200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr9:95853400-95857200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr9:95853600-95857200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr9:95853800-95857200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:95854000-95857200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr9:95854000-95857200	Enhancers	Spleen	Spleen
10	chr9:95854000-95857400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:95854000-95857400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:95854200-95857200	Weak transcription	Gastric	stomach
13	chr9:95854400-95857200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr9:95854400-95857400	Enhancers	Primary hematopoietic stem cells	blood
15	chr9:95854400-95857400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr9:95854400-95857400	Enhancers	Fetal Muscle Trunk	muscle
17	chr9:95854400-95857400	Enhancers	Fetal Muscle Leg	muscle
18	chr9:95854400-95857400	Enhancers	Placenta	Placenta
19	chr9:95854600-95857200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:95854600-95857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:95854600-95857200	Enhancers	Adipose Nuclei	Adipose
22	chr9:95854600-95857400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:95854600-95857400	Enhancers	Fetal Thymus	thymus
24	chr9:95854600-95857400	Weak transcription	NHDF-Ad	bronchial
25	chr9:95854600-95857800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr9:95854800-95857200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr9:95854800-95857200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:95854800-95857200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr9:95854800-95857200	Weak transcription	HMEC	breast
30	chr9:95854800-95857400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr9:95854800-95857400	Enhancers	Fetal Intestine Large	intestine
32	chr9:95854800-95857400	Weak transcription	NH-A	brain
33	chr9:95854800-95857800	Enhancers	Fetal Heart	heart
34	chr9:95855000-95857200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:95855000-95857200	Enhancers	Duodenum Mucosa	Duodenum
36	chr9:95855000-95857400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr9:95855000-95857400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:95855000-95857400	Enhancers	Fetal Lung	lung
39	chr9:95855000-95857400	Enhancers	Fetal Stomach	stomach
40	chr9:95855000-95857400	Enhancers	Lung	lung
41	chr9:95855000-95857400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr9:95855000-95857400	Enhancers	Right Atrium	heart
43	chr9:95855000-95857400	Weak transcription	Osteobl	bone
44	chr9:95855200-95857200	Enhancers	Brain Hippocampus Middle	brain
45	chr9:95855200-95857200	Enhancers	Fetal Kidney	kidney
46	chr9:95855200-95857200	Enhancers	Thymus	Thymus
47	chr9:95855200-95857400	Enhancers	Fetal Intestine Small	intestine
48	chr9:95855200-95857800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr9:95855400-95857200	Enhancers	Primary T cells from cord blood	blood
50	chr9:95855400-95857200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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