Variant report

Variant	rs12551405
Chromosome Location	chr9:21402393-21402394
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	CTCF	chr9:21402380-21402530	GM12865	blood:	n/a	n/a
2	SIN3A	chr9:21402384-21402507	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
IFNA12P	TF binding region
IFNA11P	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]
rs12553612	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12554005	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]
rs28383784	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21401400-21403000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
2	chr9:21402000-21402400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:21402000-21403200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:21402000-21403200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
5	chr9:21402000-21403600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
6	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
7	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
8	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
11	chr9:21402200-21402400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:21402200-21402400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
14	chr9:21402200-21402400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:21402200-21402400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr9:21402200-21402400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:21402200-21402400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:21402200-21402400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr9:21402200-21402400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:21402200-21402400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:21402200-21402400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:21402200-21402400	Bivalent Enhancer	Adipose Nuclei	Adipose
23	chr9:21402200-21402400	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr9:21402200-21402400	Bivalent Enhancer	Brain Germinal Matrix	brain
25	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
26	chr9:21402200-21402400	Active TSS	Ovary	ovary
27	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
28	chr9:21402200-21402400	Flanking Bivalent TSS/Enh	HMEC	breast
29	chr9:21402200-21402400	Bivalent Enhancer	NHEK	skin
30	chr9:21402200-21402600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:21402200-21402600	Bivalent Enhancer	Primary T cells from cord blood	blood
32	chr9:21402200-21402600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
33	chr9:21402200-21402600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr9:21402200-21402600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:21402200-21402600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
36	chr9:21402200-21402600	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr9:21402200-21402600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
38	chr9:21402200-21402600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr9:21402200-21402600	Flanking Bivalent TSS/Enh	NH-A	brain
40	chr9:21402200-21402800	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr9:21402200-21402800	Bivalent Enhancer	Fetal Lung	lung
42	chr9:21402200-21402800	Bivalent/Poised TSS	GM12878-XiMat	blood
43	chr9:21402200-21403000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:21402200-21403000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:21402200-21403000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:21402200-21403000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr9:21402200-21403000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
48	chr9:21402200-21403000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:21402200-21403000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:21402200-21403200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links