Variant report

Variant	rs12094866
Chromosome Location	chr1:154575425-154575426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154574936-154577079	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:154573055-154578396	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:154575425-154577108	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154573844..154576580-chr1:154947411..154949636,2	K562	blood:
2	chr1:154530350..154531883-chr1:154574415..154576930,2	MCF-7	breast:
3	chr1:154549225..154551805-chr1:154575345..154579789,4	MCF-7	breast:
4	chr1:154574246..154575826-chr1:154839450..154841062,2	K562	blood:
5	chr1:154574387..154584697-chr1:154596875..154603021,22	MCF-7	breast:
6	chr1:154557729..154560543-chr1:154574969..154576668,2	K562	blood:
7	chr1:154573864..154581870-chr1:154594652..154602962,18	K562	blood:

No data

Variant related genes	Relation type
ADAR	TF binding region
ENSG00000173207	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000143603	Chromatin interaction
ENSG00000160714	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11264221	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11264231	0.90[AFR][1000 genomes]
rs11264232	0.90[AFR][1000 genomes]
rs11806816	0.90[AFR][1000 genomes]
rs12079381	0.90[AFR][1000 genomes]
rs12086987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1542796	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2172708	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6677920	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6683149	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690277	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7513474	0.91[AFR][1000 genomes]
rs9427095	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
4	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154547800-154578400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154548800-154577400	Strong transcription	Fetal Intestine Small	intestine
3	chr1:154549200-154575800	Strong transcription	Brain Germinal Matrix	brain
4	chr1:154549400-154576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:154549400-154576200	Strong transcription	Primary T cells from cord blood	blood
6	chr1:154549400-154578000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:154549600-154576400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:154549800-154576400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:154549800-154576800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:154550200-154576200	Strong transcription	Thymus	Thymus
11	chr1:154550200-154576400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:154550400-154576200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:154550600-154576000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:154550800-154576000	Strong transcription	Primary B cells from cord blood	blood
15	chr1:154550800-154576000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:154550800-154578200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:154550800-154578400	Strong transcription	NHEK	skin
18	chr1:154551000-154576800	Strong transcription	Dnd41	blood
19	chr1:154551000-154577600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:154551200-154576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:154556800-154576800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:154557000-154578400	Strong transcription	Fetal Stomach	stomach
23	chr1:154557400-154577000	Strong transcription	Placenta	Placenta
24	chr1:154557600-154575600	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:154558200-154575600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:154562600-154579600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:154564200-154576800	Strong transcription	HepG2	liver
28	chr1:154569000-154576200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:154569800-154576400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:154570800-154579600	Weak transcription	Stomach Mucosa	stomach
31	chr1:154571200-154575800	Weak transcription	Small Intestine	intestine
32	chr1:154571200-154576200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:154571400-154576000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:154571400-154578400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:154571400-154578600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:154571600-154578400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:154571800-154578400	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr1:154571800-154579000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr1:154572000-154578200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr1:154572200-154578400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:154572200-154578400	Genic enhancers	Lung	lung
42	chr1:154572400-154575800	Strong transcription	Esophagus	oesophagus
43	chr1:154572400-154579000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:154572600-154575600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:154572600-154575800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:154572600-154575800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:154572600-154575800	Strong transcription	Fetal Thymus	thymus
48	chr1:154572600-154575800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:154572600-154576000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:154572600-154576000	Strong transcription	Gastric	stomach

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