Variant report

Variant	rs888601
Chromosome Location	chr9:72286253-72286254
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	chr9:72286150-72288240	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr9:72286001-72288515	SK-N-SH	brain:	n/a	chr9:72287629-72287642 chr9:72288204-72288214 chr9:72287510-72287523 chr9:72287953-72287962 chr9:72288010-72288019
3	SMC3	chr9:72286221-72288597	SK-N-SH	brain:	n/a	chr9:72286908-72286918 chr9:72287103-72287113
4	MYC	chr9:72286217-72286272	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:72286082-72288205	H1-neurons	neurons:	n/a	n/a
6	RAD21	chr9:72285926-72288545	SK-N-SH	brain:	n/a	chr9:72287629-72287643 chr9:72286908-72286918 chr9:72287509-72287523 chr9:72287335-72287348
7	REST	chr9:72286012-72288556	H1-neurons	neurons:	n/a	chr9:72287119-72287126 chr9:72288032-72288045 chr9:72287792-72287806

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72286195..72289118-chr9:72373474..72376010,3	MCF-7	breast:
2	chr9:72265675..72268152-chr9:72283798..72286751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261447	TF binding region
ENSG00000188647	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10120072	1.00[AMR][1000 genomes]
rs1023201	1.00[AMR][1000 genomes]
rs10735558	1.00[AMR][1000 genomes]
rs10867701	1.00[AMR][1000 genomes]
rs1330335	1.00[AMR][1000 genomes]
rs1576510	0.82[ASW][hapmap];1.00[AMR][1000 genomes]
rs1581958	1.00[AMR][1000 genomes]
rs1999215	1.00[AMR][1000 genomes]
rs2026384	1.00[AMR][1000 genomes]
rs2309516	1.00[AMR][1000 genomes]
rs2781534	1.00[AMR][1000 genomes]
rs4409461	1.00[AMR][1000 genomes]
rs4744573	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs4744916	1.00[AMR][1000 genomes]
rs4744925	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs4744929	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56399720	1.00[AMR][1000 genomes]
rs6559653	0.82[ASW][hapmap];1.00[AMR][1000 genomes]
rs7036621	1.00[AMR][1000 genomes]
rs7045100	1.00[AMR][1000 genomes]
rs7853119	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs7854208	1.00[AMR][1000 genomes]
rs7856525	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs7862740	0.81[AFR][1000 genomes]
rs7865174	1.00[AMR][1000 genomes]
rs7866895	1.00[AMR][1000 genomes]
rs7869217	1.00[AMR][1000 genomes]
rs918338	1.00[AMR][1000 genomes]
rs9410853	1.00[AMR][1000 genomes]
rs987417	1.00[AMR][1000 genomes]
rs987418	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3389299	chr9:72286157-72289005	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72283800-72286400	Weak transcription	Right Atrium	heart
2	chr9:72285200-72286600	Flanking Active TSS	Fetal Brain Female	brain
3	chr9:72285400-72286600	Flanking Active TSS	Fetal Brain Male	brain
4	chr9:72285400-72286800	Flanking Active TSS	Liver	Liver
5	chr9:72285400-72288400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:72285600-72286600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr9:72285600-72286600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:72285600-72286600	Bivalent Enhancer	Spleen	Spleen
9	chr9:72285800-72286400	Enhancers	Right Ventricle	heart
10	chr9:72286000-72286400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr9:72286000-72286400	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr9:72286000-72286400	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr9:72286000-72286400	Flanking Active TSS	Fetal Stomach	stomach
14	chr9:72286000-72286600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:72286000-72286600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:72286000-72286600	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr9:72286000-72286600	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr9:72286000-72286600	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr9:72286000-72286600	Flanking Active TSS	Fetal Kidney	kidney
20	chr9:72286000-72286600	Flanking Active TSS	Fetal Lung	lung
21	chr9:72286000-72286600	Flanking Active TSS	NHDF-Ad	bronchial
22	chr9:72286000-72286800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:72286000-72286800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr9:72286000-72286800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr9:72286000-72287000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr9:72286000-72287600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr9:72286000-72288200	Active TSS	Brain Substantia Nigra	brain
28	chr9:72286200-72286400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
29	chr9:72286200-72286400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:72286200-72286400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
31	chr9:72286200-72286400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:72286200-72286400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:72286200-72286400	Enhancers	Aorta	Aorta
34	chr9:72286200-72286400	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr9:72286200-72286400	Enhancers	Esophagus	oesophagus
36	chr9:72286200-72286400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr9:72286200-72286400	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr9:72286200-72286400	Enhancers	Placenta	Placenta
39	chr9:72286200-72286400	Enhancers	Left Ventricle	heart
40	chr9:72286200-72286400	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr9:72286200-72286600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
42	chr9:72286200-72286600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:72286200-72286600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:72286200-72286600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:72286200-72286600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:72286200-72286600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:72286200-72286600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr9:72286200-72286600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:72286200-72286600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:72286200-72286600	Flanking Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links