Variant report

Variant	rs12888372
Chromosome Location	chr14:55119599-55119600
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55032687..55034236-chr14:55119438..55121090,2	MCF-7	breast:
2	chr14:55119482..55121341-chr14:55121641..55124299,2	MCF-7	breast:
3	chr14:55031461..55035668-chr14:55117629..55122192,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000020577	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11158019	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12586228	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12586646	0.98[ASN][1000 genomes]
rs12586705	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12590927	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890352	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17728293	0.96[CEU][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2025130	0.81[CEU][hapmap];0.87[ASN][1000 genomes]
rs35399674	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4553503	0.86[ASN][1000 genomes]
rs4898844	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7151563	0.87[ASN][1000 genomes]
rs7155089	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7158091	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8011374	0.84[CEU][hapmap]
rs8022597	0.81[ASN][1000 genomes]
rs911621	0.93[ASN][1000 genomes]
rs942607	0.81[CEU][hapmap];0.94[EUR][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	nsv974464	chr14:55092217-55152792	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55107600-55121400	Weak transcription	Pancreas	Pancrea
2	chr14:55109600-55121400	Weak transcription	Spleen	Spleen
3	chr14:55110800-55119600	Weak transcription	Lung	lung
4	chr14:55113200-55122000	Enhancers	Fetal Heart	heart
5	chr14:55114800-55120200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:55116000-55121400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:55116200-55122000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr14:55116400-55119600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:55116600-55121600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:55116800-55119800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr14:55116800-55120000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr14:55117000-55120000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:55117000-55121000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr14:55117000-55121600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:55117000-55121600	Enhancers	Placenta	Placenta
16	chr14:55117200-55119800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:55117200-55120000	Enhancers	Fetal Stomach	stomach
18	chr14:55117200-55121600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:55117600-55119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr14:55117600-55119800	Enhancers	Liver	Liver
21	chr14:55117600-55121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:55117600-55129400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr14:55117800-55120400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr14:55117800-55120400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr14:55118000-55120000	Enhancers	Fetal Intestine Small	intestine
26	chr14:55118000-55120200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr14:55118000-55120400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr14:55118200-55119600	Weak transcription	Right Ventricle	heart
29	chr14:55118200-55120400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:55118200-55120600	Weak transcription	Colonic Mucosa	Colon
31	chr14:55118400-55119600	Enhancers	Brain Substantia Nigra	brain
32	chr14:55118400-55119800	Enhancers	Fetal Kidney	kidney
33	chr14:55118400-55120000	Flanking Active TSS	HUVEC	blood vessel
34	chr14:55118400-55120000	Flanking Active TSS	NHEK	skin
35	chr14:55118400-55121400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr14:55118600-55119600	Active TSS	Right Atrium	heart
37	chr14:55118600-55120000	Enhancers	Fetal Intestine Large	intestine
38	chr14:55118800-55119600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr14:55118800-55119600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:55118800-55119600	Active TSS	Aorta	Aorta
41	chr14:55118800-55119800	Enhancers	H1 Cell Line	embryonic stem cell
42	chr14:55118800-55119800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:55118800-55119800	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr14:55118800-55119800	Active TSS	Fetal Brain Male	brain
45	chr14:55118800-55119800	Flanking Active TSS	Fetal Lung	lung
46	chr14:55118800-55119800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr14:55118800-55120000	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr14:55118800-55120000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr14:55119000-55119600	Active TSS	Brain Hippocampus Middle	brain
50	chr14:55119000-55119600	Active TSS	Brain Inferior Temporal Lobe	brain

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