Variant report

Variant	rs3739682
Chromosome Location	chr9:33466525-33466526
allele	A/C/G/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	CTCF	chr9:33466522-33467081	MCF-7	breast:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
2	CTCF	chr9:33466477-33466991	GM19238	blood:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
3	RAD21	chr9:33466360-33467067	A549	lung:	n/a	chr9:33466796-33466815
4	RAD21	chr9:33466364-33467221	HCT-116	colon:	n/a	chr9:33466796-33466815
5	CTCF	chr9:33466247-33467308	A549	lung:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
6	CTCF	chr9:33466525-33467042	A549	lung:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
7	CTCF	chr9:33466464-33467061	HCT-116	colon:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
8	POLR2A	chr9:33466400-33466914	GM12878	blood:	n/a	n/a
9	RAD21	chr9:33466463-33467010	H1-hESC	embryonic stem cell:	n/a	chr9:33466796-33466815
10	RAD21	chr9:33466466-33467103	MCF-7	breast:	n/a	chr9:33466796-33466815
11	RAD21	chr9:33466378-33467165	HCT-116	colon:	n/a	chr9:33466796-33466815
12	CTCF	chr9:33466288-33467503	SK-N-SH	brain:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
13	CTCF	chr9:33466512-33466593	GM19239	blood:	n/a	n/a
14	CTCF	chr9:33466212-33467198	HCT-116	colon:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
15	RAD21	chr9:33466415-33467153	SK-N-SH	brain:	n/a	chr9:33466796-33466815
16	RAD21	chr9:33466492-33467100	ECC-1	luminal epithelium:	n/a	chr9:33466796-33466815
17	RAD21	chr9:33466486-33467069	MCF-7	breast:	n/a	chr9:33466796-33466815
18	CTCF	chr9:33466495-33466978	GM12892	blood:	n/a	chr9:33466800-33466813 chr9:33466798-33466816
19	SMC3	chr9:33466293-33467163	SK-N-SH	brain:	n/a	chr9:33466800-33466814 chr9:33466803-33466813 chr9:33466800-33466810
20	TCF12	chr9:33466515-33467038	A549	lung:	n/a	n/a
21	CTCF	chr9:33466481-33466982	GM12891	blood:	n/a	chr9:33466800-33466813 chr9:33466798-33466816

No.	Distal block	Cell Line	Cell type
1	chr9:33410830..33412898-chr9:33466360..33468134,2	MCF-7	breast:
2	chr9:33289187..33291414-chr9:33465328..33466837,2	MCF-7	breast:
3	chr9:33465669..33469321-chr9:33471181..33475399,6	K562	blood:
4	chr9:33401937..33405021-chr9:33465518..33470262,4	MCF-7	breast:
5	chr9:33403047..33404002-chr9:33466342..33467383,7	MCF-7	breast:
6	chr9:33465249..33467402-chr9:33478789..33481100,2	MCF-7	breast:
7	chr9:33444170..33447177-chr9:33466129..33468559,3	MCF-7	breast:

Variant related genes	Relation type
NOL6	TF binding region
ENSG00000165269	Chromatin interaction
ENSG00000223678	Chromatin interaction
ENSG00000165271	Chromatin interaction
ENSG00000086102	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10465079	0.83[EUR][1000 genomes]
rs10813986	1.00[EUR][1000 genomes]
rs10971528	1.00[EUR][1000 genomes]
rs10971529	1.00[EUR][1000 genomes]
rs10971532	1.00[EUR][1000 genomes]
rs10971533	1.00[EUR][1000 genomes]
rs10971537	1.00[EUR][1000 genomes]
rs10971539	1.00[EUR][1000 genomes]
rs10971542	1.00[EUR][1000 genomes]
rs3814514	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7027139	1.00[EUR][1000 genomes]
rs7031985	1.00[EUR][1000 genomes]
rs7033723	1.00[EUR][1000 genomes]
rs7038544	1.00[EUR][1000 genomes]
rs7043800	1.00[EUR][1000 genomes]
rs73482880	1.00[EUR][1000 genomes]
rs7861182	1.00[EUR][1000 genomes]
rs7864131	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024207	chr9:33296368-33574892	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1024571	chr9:33380148-33468682	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1015928	chr9:33386067-33468682	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv516500	chr9:33434931-33466859	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv518168	chr9:33465182-33478434	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv527128	chr9:33465651-33467595	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:33448400-33473000	Weak transcription	Right Atrium	heart
2	chr9:33453000-33469400	Weak transcription	Fetal Heart	heart
3	chr9:33453600-33473200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:33458800-33467200	Genic enhancers	NHEK	skin
5	chr9:33459400-33472200	Strong transcription	Fetal Brain Female	brain
6	chr9:33459600-33472200	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:33459800-33468200	Weak transcription	Fetal Brain Male	brain
8	chr9:33460000-33467200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:33460000-33470400	Strong transcription	Thymus	Thymus
10	chr9:33460000-33470600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:33460000-33472000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr9:33460000-33472000	Strong transcription	Fetal Stomach	stomach
13	chr9:33460000-33472200	Strong transcription	Fetal Intestine Large	intestine
14	chr9:33460000-33472200	Strong transcription	Fetal Intestine Small	intestine
15	chr9:33460000-33472200	Strong transcription	Fetal Muscle Leg	muscle
16	chr9:33460200-33466800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:33460200-33471400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:33460200-33471600	Strong transcription	HSMM	muscle
19	chr9:33460200-33471800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:33460200-33471800	Strong transcription	Brain Germinal Matrix	brain
21	chr9:33460200-33471800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:33460200-33471800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:33460200-33472000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:33460200-33472000	Strong transcription	Brain Anterior Caudate	brain
25	chr9:33460200-33472000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:33460200-33472000	Strong transcription	Placenta	Placenta
27	chr9:33460200-33472000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr9:33460200-33472200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:33460200-33472200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:33460200-33472400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:33460400-33466600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:33460400-33466800	Strong transcription	Liver	Liver
33	chr9:33460400-33470800	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr9:33460400-33471200	Strong transcription	Primary T cells from cord blood	blood
35	chr9:33460400-33471200	Strong transcription	NH-A	brain
36	chr9:33460400-33471400	Strong transcription	Brain Angular Gyrus	brain
37	chr9:33460400-33471600	Strong transcription	Osteobl	bone
38	chr9:33460400-33472000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:33460400-33472000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:33460400-33472000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr9:33460400-33472000	Strong transcription	Gastric	stomach
42	chr9:33460400-33472200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr9:33460400-33472200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:33460400-33472200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:33460600-33470400	Strong transcription	Spleen	Spleen
46	chr9:33460600-33470800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:33460600-33471400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:33460600-33471600	Strong transcription	GM12878-XiMat	blood
49	chr9:33460600-33471800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:33460600-33471800	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links