Variant report

Variant	rs28547922
Chromosome Location	chr14:105881925-105881926
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr14:105881296-105882049	A549	lung:	n/a	chr14:105881615-105881624 chr14:105881613-105881622 chr14:105881612-105881626
2	POLR2A	chr14:105880579-105882910	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:105879052-105882017	SK-N-MC	brain:	n/a	n/a
4	CTCF	chr14:105881176-105882122	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr14:105881109-105881928	A549	lung:	n/a	n/a
6	POLR2A	chr14:105881818-105881938	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr14:105881718-105882104	MCF10A-Er-Src	breast:	n/a	n/a
8	HCFC1	chr14:105881038-105882083	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:105880098..105883003-chr14:105910883..105913200,2	K562	blood:
2	chr14:105876338..105883262-chr14:105952928..105958741,9	MCF-7	breast:
3	chr14:105865246..105867543-chr14:105880799..105882893,2	K562	blood:
4	chr14:105859207..105862401-chr14:105879269..105882995,3	K562	blood:
5	chr14:105833305..105836227-chr14:105880754..105883670,2	K562	blood:
6	chr14:105881282..105882070-chr6:27804848..27805770,2	NB4	blood:
7	chr14:105878253..105887592-chr14:105952988..105961277,12	MCF-7	breast:
8	chr14:105859207..105861741-chr14:105880044..105882995,2	K562	blood:
9	chr14:105878872..105884276-chr14:105939558..105943133,6	MCF-7	breast:

No data

Variant related genes	Relation type
MTA1	TF binding region
ENSG00000213145	Chromatin interaction
ENSG00000185347	Chromatin interaction
ENSG00000182809	Chromatin interaction
ENSG00000257341	Chromatin interaction
ENSG00000256498	Chromatin interaction
ENSG00000179364	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10132193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10133343	1.00[AMR][1000 genomes]
rs10133666	1.00[AMR][1000 genomes]
rs10136894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10137499	1.00[AMR][1000 genomes]
rs10142763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10150076	1.00[AMR][1000 genomes]
rs10151345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10152000	1.00[AMR][1000 genomes]
rs11847920	1.00[AMR][1000 genomes]
rs11850681	1.00[AMR][1000 genomes]
rs11850746	1.00[AMR][1000 genomes]
rs28406946	1.00[AMR][1000 genomes]
rs28419155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28451686	1.00[AMR][1000 genomes]
rs28482150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507499	1.00[AMR][1000 genomes]
rs28537945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28539444	1.00[AMR][1000 genomes]
rs28545230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28588179	1.00[AMR][1000 genomes]
rs28665678	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28678078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28678492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28710336	1.00[AMR][1000 genomes]
rs28733380	1.00[AMR][1000 genomes]
rs28741003	0.85[AFR][1000 genomes]
rs4073351	1.00[AMR][1000 genomes]
rs4073352	1.00[AMR][1000 genomes]
rs56734561	1.00[AMR][1000 genomes]
rs61326617	1.00[AMR][1000 genomes]
rs7158718	1.00[AMR][1000 genomes]
rs73361045	1.00[AMR][1000 genomes]
rs8009536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8009750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9743768	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9989145	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530813	chr14:105607701-106453697	Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105878200-105885200	Weak transcription	NHDF-Ad	bronchial
2	chr14:105880000-105882000	Enhancers	Liver	Liver
3	chr14:105880800-105882000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr14:105880800-105882000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:105880800-105882000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr14:105880800-105882000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:105880800-105882000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:105880800-105882000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr14:105880800-105882200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr14:105880800-105882200	Active TSS	Fetal Brain Female	brain
11	chr14:105880800-105882600	Enhancers	Fetal Heart	heart
12	chr14:105880800-105882600	Flanking Active TSS	Dnd41	blood
13	chr14:105881000-105882000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr14:105881000-105882000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr14:105881000-105882000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:105881000-105882000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr14:105881000-105882000	Active TSS	Brain Angular Gyrus	brain
18	chr14:105881000-105882000	Active TSS	Brain Hippocampus Middle	brain
19	chr14:105881000-105882000	Enhancers	Placenta	Placenta
20	chr14:105881000-105882000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr14:105881000-105882000	Active TSS	Thymus	Thymus
22	chr14:105881000-105882000	Active TSS	NHEK	skin
23	chr14:105881200-105882000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr14:105881200-105882000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr14:105881200-105882000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr14:105881200-105882000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:105881200-105882000	Active TSS	Fetal Kidney	kidney
28	chr14:105881200-105882000	Active TSS	Placenta Amnion	Placenta Amnion
29	chr14:105881200-105882000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr14:105881200-105882000	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr14:105881200-105882000	Active TSS	K562	blood
32	chr14:105881200-105882000	Active TSS	NH-A	brain
33	chr14:105881400-105882000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr14:105881400-105882000	Active TSS	HSMMtube	muscle
35	chr14:105881600-105882000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr14:105881600-105882000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr14:105881600-105882000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr14:105881600-105882000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr14:105881600-105882000	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr14:105881600-105882000	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr14:105881600-105882000	Weak transcription	Esophagus	oesophagus
42	chr14:105881600-105882000	Flanking Active TSS	Fetal Brain Male	brain
43	chr14:105881600-105882000	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr14:105881600-105882000	Flanking Active TSS	Fetal Stomach	stomach
45	chr14:105881600-105882000	Weak transcription	Spleen	Spleen
46	chr14:105881600-105882200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
47	chr14:105881600-105882200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr14:105881600-105884600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:105881600-105884600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr14:105881600-105885000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links