Variant report

Variant	rs12554005
Chromosome Location	chr9:21402655-21402656
allele	C/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	CTCF	chr9:21402580-21402870	HAc	cerebellar:	n/a	n/a
2	E2F6	chr9:21402647-21403351	H1-hESC	embryonic stem cell:	n/a	chr9:21402875-21402892 chr9:21402875-21402892 chr9:21402878-21402889
3	CTCF	chr9:21402640-21402790	AG04450	lung:	n/a	n/a
4	CTCF	chr9:21402640-21402790	A549	lung:	n/a	n/a
5	EBF1	chr9:21402597-21402928	GM12878	blood:	n/a	chr9:21402802-21402812 chr9:21402746-21402755 chr9:21402746-21402756 chr9:21402745-21402756 chr9:21402800-21402811
6	TBP	chr9:21402488-21403114	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr9:21402647-21403318	A549	lung:	n/a	chr9:21402875-21402892 chr9:21402875-21402892 chr9:21402878-21402889
8	MAX	chr9:21402639-21403390	A549	lung:	n/a	n/a
9	EBF1	chr9:21402643-21402997	GM12878	blood:	n/a	chr9:21402802-21402812 chr9:21402746-21402755 chr9:21402746-21402756 chr9:21402745-21402756 chr9:21402800-21402811
10	EBF1	chr9:21402526-21403142	GM12878	blood:	n/a	chr9:21402802-21402812 chr9:21402746-21402755 chr9:21402746-21402756 chr9:21402745-21402756 chr9:21402800-21402811

Variant related genes	Relation type
IFNA11P	TF binding region
IFNA12P	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10964972	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10964973	0.82[AMR][1000 genomes]
rs12551405	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12553612	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs28383784	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892737	chr9:21352862-21408824	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2752289	chr9:21361957-21499624	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892738	chr9:21371264-21413085	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv466297	chr9:21391698-21507589	Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv613758	chr9:21391698-21507589	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21401400-21403000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
2	chr9:21402000-21403200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr9:21402000-21403200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
4	chr9:21402000-21403600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
5	chr9:21402200-21402800	Flanking Active TSS	Brain Angular Gyrus	brain
6	chr9:21402200-21402800	Bivalent Enhancer	Fetal Lung	lung
7	chr9:21402200-21402800	Bivalent/Poised TSS	GM12878-XiMat	blood
8	chr9:21402200-21403000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:21402200-21403000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:21402200-21403000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:21402200-21403000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:21402200-21403000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr9:21402200-21403000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:21402200-21403000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:21402200-21403200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:21402200-21403200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr9:21402200-21403200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr9:21402200-21403200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:21402200-21403200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:21402200-21403200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
21	chr9:21402200-21403200	Bivalent/Poised TSS	A549	lung
22	chr9:21402200-21403200	Bivalent/Poised TSS	NHDF-Ad	bronchial
23	chr9:21402200-21403400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:21402400-21402800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:21402400-21402800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:21402400-21402800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr9:21402400-21402800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:21402400-21402800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:21402400-21402800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr9:21402400-21402800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr9:21402400-21402800	Bivalent Enhancer	Left Ventricle	heart
32	chr9:21402400-21402800	Bivalent/Poised TSS	Thymus	Thymus
33	chr9:21402400-21402800	Bivalent/Poised TSS	HMEC	breast
34	chr9:21402400-21403000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:21402400-21403000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr9:21402400-21403000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:21402400-21403000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:21402400-21403000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
39	chr9:21402400-21403000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
40	chr9:21402400-21403000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
41	chr9:21402400-21403000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
42	chr9:21402400-21403000	Bivalent/Poised TSS	Esophagus	oesophagus
43	chr9:21402400-21403000	Bivalent/Poised TSS	Fetal Brain Female	brain
44	chr9:21402400-21403000	Bivalent Enhancer	Lung	lung
45	chr9:21402400-21403000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
46	chr9:21402400-21403000	Active TSS	Right Ventricle	heart
47	chr9:21402400-21403000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr9:21402400-21403000	Flanking Bivalent TSS/Enh	NHEK	skin
49	chr9:21402400-21403200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr9:21402400-21403200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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