Variant report

Variant	rs534725294
Chromosome Location	chr9:86432257-86432258
allele	A/C
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	CTCF	chr9:86432251-86432412	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr9:86432180-86432330	AG04450	lung:	n/a	n/a
3	CTCF	chr9:86432240-86432390	HRPEpiC	eye:	n/a	n/a
4	CTCF	chr9:86432220-86432370	AG09309	skin:	n/a	n/a
5	CTCF	chr9:86432133-86432657	K562	blood:	n/a	n/a
6	CTCF	chr9:86432240-86432390	GM12875	blood:	n/a	n/a
7	RAD21	chr9:86432231-86432422	HepG2	liver:	n/a	chr9:86432267-86432279 chr9:86432326-86432340 chr9:86432328-86432341
8	CTCF	chr9:86432200-86432350	RPTEC	kidney:	n/a	n/a
9	ZBTB7A	chr9:86432168-86432376	K562	blood:	n/a	n/a
10	CTCF	chr9:86432244-86432464	GM19240	blood:	n/a	n/a
11	CTCF	chr9:86432240-86432390	GM12865	blood:	n/a	n/a
12	CCNT2	chr9:86432252-86432698	K562	blood:	n/a	chr9:86432668-86432677
13	POLR2A	chr9:86432089-86432745	GM12878	blood:	n/a	n/a
14	POLR2A	chr9:86432189-86432741	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr9:86432220-86432370	K562	blood:	n/a	n/a
16	HCFC1	chr9:86432204-86432539	K562	blood:	n/a	n/a
17	POLR2A	chr9:86432121-86433131	A549	lung:	n/a	n/a
18	TCF12	chr9:86432075-86432318	GM12878	blood:	n/a	n/a
19	CTCF	chr9:86432208-86432486	K562	blood:	n/a	n/a
20	E2F6	chr9:86432223-86432426	K562	blood:	n/a	n/a
21	CTCF	chr9:86432240-86432390	HCFaa	heart:	n/a	n/a
22	POLR2A	chr9:86432057-86432750	GM12878	blood:	n/a	n/a
23	EBF1	chr9:86432126-86432356	GM12878	blood:	n/a	n/a
24	POLR2A	chr9:86432249-86433148	Hela-S3	cervix:	n/a	n/a
25	ZKSCAN1	chr9:86432244-86432380	Hela-S3	cervix:	n/a	n/a
26	HA-E2F1	chr9:86431867-86433290	MCF-7	breast:	n/a	chr9:86432114-86432124 chr9:86432222-86432231 chr9:86432475-86432484 chr9:86432476-86432486
27	POLR2A	chr9:86432103-86433547	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr9:86432200-86432821	ProgFib	skin:	n/a	n/a
29	POLR2A	chr9:86432144-86432709	GM12878	blood:	n/a	n/a
30	PAX5	chr9:86432184-86432447	GM12878	blood:	n/a	n/a
31	POLR2A	chr9:86432138-86433041	A549	lung:	n/a	n/a
32	CTCF	chr9:86432220-86432370	AG09319	gingival:	n/a	n/a
33	CTCF	chr9:86432240-86432390	GM12867	blood:	n/a	n/a
34	CTCF	chr9:86432220-86432370	AoAF	blood vessel:	n/a	n/a
35	CTCF	chr9:86432246-86432470	GM19239	blood:	n/a	n/a
36	HEY1	chr9:86432168-86433255	HepG2	liver:	n/a	chr9:86432474-86432489 chr9:86432783-86432798 chr9:86432672-86432687 chr9:86432829-86432844 chr9:86432790-86432805
37	TCF3	chr9:86432044-86432728	GM12878	blood:	n/a	chr9:86432141-86432151
38	CTCF	chr9:86432220-86432370	NHLF	lung:	n/a	n/a
39	POLR2A	chr9:86432096-86433143	A549	lung:	n/a	n/a
40	HMGN3	chr9:86432161-86432533	K562	blood:	n/a	n/a
41	MAX	chr9:86432248-86432305	HepG2	liver:	n/a	n/a
42	UBTF	chr9:86432045-86433000	K562	blood:	n/a	n/a
43	POLR2A	chr9:86432108-86433024	MCF-7	breast:	n/a	n/a
44	SIN3AK20	chr9:86431865-86432345	SK-N-SH	brain:	n/a	n/a
45	RAD21	chr9:86432206-86432431	K562	blood:	n/a	chr9:86432267-86432279 chr9:86432326-86432340 chr9:86432328-86432341
46	CTCF	chr9:86432220-86432370	HPF	lung:	n/a	n/a
47	HEY1	chr9:86432192-86432312	HepG2	liver:	n/a	n/a
48	POLR2A	chr9:86432235-86432768	Gliobla	brain:	n/a	n/a
49	POLR2A	chr9:86432149-86432809	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr9:86432151-86432741	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86430622..86432919-chr9:86535075..86537489,2	MCF-7	breast:
2	chr9:86321555..86324208-chr9:86431445..86433817,2	MCF-7	breast:
3	chr9:86321469..86324662-chr9:86431245..86433854,3	MCF-7	breast:

Variant related genes	Relation type
GKAP1	TF binding region
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2761538	chr9:86401015-86451943	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3331113	chr9:86431782-86433830	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86431000-86433000	Active TSS	A549	lung
2	chr9:86431000-86433200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:86431000-86433200	Active TSS	Aorta	Aorta
4	chr9:86431000-86433200	Active TSS	GM12878-XiMat	blood
5	chr9:86431000-86433200	Active TSS	Hela-S3	cervix
6	chr9:86431200-86433000	Active TSS	NHDF-Ad	bronchial
7	chr9:86431200-86433200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:86431200-86433400	Active TSS	Thymus	Thymus
9	chr9:86431400-86432400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr9:86431400-86433000	Active TSS	NHLF	lung
11	chr9:86431400-86433200	Active TSS	Fetal Muscle Leg	muscle
12	chr9:86431400-86433200	Active TSS	HepG2	liver
13	chr9:86431400-86433400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:86431400-86433400	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr9:86431400-86433400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr9:86431600-86432800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr9:86431600-86433000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:86431600-86433000	Active TSS	Primary T cells fromperipheralblood	blood
19	chr9:86431600-86433000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:86431600-86433000	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr9:86431600-86433000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:86431600-86433000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr9:86431600-86433000	Active TSS	Fetal Muscle Trunk	muscle
24	chr9:86431600-86433000	Active TSS	Fetal Thymus	thymus
25	chr9:86431600-86433000	Active TSS	NH-A	brain
26	chr9:86431600-86433000	Active TSS	NHEK	skin
27	chr9:86431600-86433000	Active TSS	Osteobl	bone
28	chr9:86431600-86433200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:86431600-86433200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:86431600-86433200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:86431600-86433200	Active TSS	Brain Anterior Caudate	brain
32	chr9:86431600-86433200	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr9:86431600-86433200	Active TSS	Fetal Intestine Large	intestine
34	chr9:86431600-86433200	Active TSS	Fetal Stomach	stomach
35	chr9:86431600-86433200	Active TSS	Ovary	ovary
36	chr9:86431600-86433200	Active TSS	Psoas Muscle	Psoas
37	chr9:86431600-86433200	Active TSS	Rectal Smooth Muscle	rectum
38	chr9:86431600-86433200	Active TSS	Right Atrium	heart
39	chr9:86431600-86433200	Active TSS	Right Ventricle	heart
40	chr9:86431600-86433200	Active TSS	K562	blood
41	chr9:86431600-86433400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr9:86431600-86433400	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr9:86431600-86433400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr9:86431600-86433400	Active TSS	Colonic Mucosa	Colon
45	chr9:86431600-86433400	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr9:86431600-86433400	Active TSS	HSMMtube	muscle
47	chr9:86431600-86433800	Active TSS	Stomach Smooth Muscle	stomach
48	chr9:86431800-86432800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:86431800-86433000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:86431800-86433000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links