Variant report

Variant	rs12890357
Chromosome Location	chr14:70481932-70481933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70464835..70467780-chr14:70480239..70482134,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10134291	0.90[ASN][1000 genomes]
rs10134965	0.90[ASN][1000 genomes]
rs11158827	0.84[ASN][1000 genomes]
rs1156446	0.81[AMR][1000 genomes]
rs12050076	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12050089	0.90[ASN][1000 genomes]
rs12101270	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12885068	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12885683	0.90[ASN][1000 genomes]
rs12887943	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12889195	0.90[ASN][1000 genomes]
rs1459704	0.90[ASN][1000 genomes]
rs17107547	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17107592	0.92[AMR][1000 genomes]
rs17107610	0.85[ASN][1000 genomes]
rs1998334	0.81[AMR][1000 genomes]
rs227437	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34311408	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825739	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55784307	0.81[AMR][1000 genomes]
rs56031625	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56242824	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57609901	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60011612	0.89[AMR][1000 genomes]
rs67294558	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7141378	0.89[ASN][1000 genomes]
rs7157226	0.89[ASN][1000 genomes]
rs7160726	0.89[ASN][1000 genomes]
rs72728002	0.81[AMR][1000 genomes]
rs72729803	0.81[AMR][1000 genomes]
rs8012912	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70457800-70484800	Weak transcription	Brain Substantia Nigra	brain
2	chr14:70459000-70484800	Weak transcription	Gastric	stomach
3	chr14:70466200-70484800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr14:70468400-70484400	Weak transcription	A549	lung
5	chr14:70469800-70484800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:70472400-70485400	Strong transcription	Hela-S3	cervix
7	chr14:70475800-70484800	Weak transcription	Brain Hippocampus Middle	brain
8	chr14:70475800-70487200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr14:70476000-70500000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr14:70476200-70482200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:70476200-70490600	Weak transcription	Fetal Brain Male	brain
12	chr14:70476200-70499000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:70477000-70483000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:70477000-70484200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr14:70477400-70484600	Weak transcription	Fetal Stomach	stomach
16	chr14:70478400-70484200	Weak transcription	NHEK	skin
17	chr14:70478400-70484800	Weak transcription	Brain Anterior Caudate	brain
18	chr14:70478600-70484200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:70478600-70484400	Weak transcription	Spleen	Spleen
20	chr14:70479000-70484000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr14:70480000-70484600	Strong transcription	Liver	Liver
22	chr14:70480400-70482000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr14:70480600-70482000	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:70480600-70482200	Strong transcription	HepG2	liver
25	chr14:70481000-70485200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:70481200-70483200	Weak transcription	Fetal Brain Female	brain
27	chr14:70481400-70482000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:70481400-70482000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr14:70481400-70482400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:70481600-70483600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:70481600-70484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:70481600-70488200	Weak transcription	Brain Germinal Matrix	brain
33	chr14:70481800-70482000	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links