Variant report

Variant	rs13290598
Chromosome Location	chr9:2624433-2624434
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	CEBPB	chr9:2624344-2624623	Hela-S3	cervix:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
2	POLR2A	chr9:2622073-2625205	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr9:2624376-2624611	MCF-7	breast:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
4	CEBPB	chr9:2624317-2624652	K562	blood:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
5	WRNIP1	chr9:2624340-2624434	GM12878	blood:	n/a	n/a
6	MXI1	chr9:2619904-2624722	SK-N-SH	brain:	n/a	n/a
7	CEBPB	chr9:2623681-2624674	A549	lung:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2623970-2623983 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
8	CEBPB	chr9:2624289-2624719	A549	lung:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
9	CEBPB	chr9:2624309-2624662	HepG2	liver:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
10	CEBPB	chr9:2624305-2624658	IMR90	lung:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496
11	CEBPB	chr9:2624354-2624556	H1-hESC	embryonic stem cell:	n/a	chr9:2624483-2624494 chr9:2624485-2624496 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624494 chr9:2624485-2624496 chr9:2624483-2624496 chr9:2624483-2624496 chr9:2624483-2624496

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2622798..2625667-chr9:2640741..2642429,2	K562	blood:
2	chr9:2620987..2624573-chr9:2639977..2643677,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236404	TF binding region
ENSG00000236404	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs7022086	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7022122	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv892069	chr9:2600836-2631738	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv892070	chr9:2610307-2633921	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv892071	chr9:2618969-2626031	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv892073	chr9:2620592-2627365	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv527298	chr9:2621030-2631092	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv892074	chr9:2623615-2629776	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2621400-2624800	Active TSS	Stomach Smooth Muscle	stomach
2	chr9:2623000-2625000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr9:2623000-2625200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr9:2623600-2626600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:2623800-2624600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:2623800-2630400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:2623800-2641000	Weak transcription	Esophagus	oesophagus
8	chr9:2624000-2624800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:2624000-2624800	Enhancers	Brain Cingulate Gyrus	brain
10	chr9:2624000-2625000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:2624000-2625000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr9:2624000-2625000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:2624000-2625000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
14	chr9:2624000-2625000	Flanking Active TSS	Ovary	ovary
15	chr9:2624000-2625000	Enhancers	Right Atrium	heart
16	chr9:2624000-2625400	Enhancers	Brain Angular Gyrus	brain
17	chr9:2624000-2627200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:2624000-2630000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:2624000-2636000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:2624200-2624600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:2624200-2624600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
22	chr9:2624200-2624600	Enhancers	Brain Substantia Nigra	brain
23	chr9:2624200-2624600	Enhancers	Fetal Lung	lung
24	chr9:2624200-2624800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:2624200-2624800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:2624200-2624800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:2624200-2624800	Enhancers	Brain Anterior Caudate	brain
28	chr9:2624200-2624800	Enhancers	Brain Hippocampus Middle	brain
29	chr9:2624200-2625000	Enhancers	Left Ventricle	heart
30	chr9:2624200-2625000	Enhancers	Psoas Muscle	Psoas
31	chr9:2624200-2625200	Enhancers	Fetal Brain Male	brain
32	chr9:2624200-2630000	Weak transcription	Gastric	stomach
33	chr9:2624200-2631600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:2624200-2633800	Weak transcription	Fetal Stomach	stomach
35	chr9:2624200-2635200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:2624200-2635200	Enhancers	Fetal Heart	heart
37	chr9:2624200-2635600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:2624200-2636000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:2624200-2641000	Weak transcription	Aorta	Aorta
40	chr9:2624400-2624600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr9:2624400-2624800	Enhancers	A549	lung
42	chr9:2624400-2625000	Enhancers	Pancreas	Pancrea
43	chr9:2624400-2625000	Flanking Active TSS	Dnd41	blood
44	chr9:2624400-2625200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr9:2624400-2625600	Enhancers	Right Ventricle	heart
46	chr9:2624400-2625800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:2624400-2627000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:2624400-2632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:2624400-2632200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:2624400-2641200	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links