Variant report

Variant	rs56006015
Chromosome Location	chr16:46961531-46961532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009391	0.85[EUR][1000 genomes]
rs11860484	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11861896	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12931259	0.83[EUR][1000 genomes]
rs12934580	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12935606	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869006	0.94[EUR][1000 genomes]
rs2192644	0.91[EUR][1000 genomes]
rs35354454	0.81[EUR][1000 genomes]
rs4246381	0.92[EUR][1000 genomes]
rs4966706	0.94[EUR][1000 genomes]
rs4966708	0.94[EUR][1000 genomes]
rs4966710	0.97[EUR][1000 genomes]
rs4966713	0.99[EUR][1000 genomes]
rs4967576	0.85[EUR][1000 genomes]
rs4967602	0.95[EUR][1000 genomes]
rs4967621	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56042735	0.95[EUR][1000 genomes]
rs56354199	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57127559	0.90[EUR][1000 genomes]
rs58074838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59708508	0.85[EUR][1000 genomes]
rs62057633	0.85[EUR][1000 genomes]
rs6598777	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67211229	0.90[EUR][1000 genomes]
rs67369452	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7186748	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7192574	0.95[EUR][1000 genomes]
rs7196375	0.89[EUR][1000 genomes]
rs7197485	0.87[EUR][1000 genomes]
rs72812428	0.94[EUR][1000 genomes]
rs73545757	0.82[AFR][1000 genomes]
rs8053137	0.88[EUR][1000 genomes]
rs9328668	0.90[EUR][1000 genomes]
rs9889198	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	esv1831215	chr16:46907546-46962858	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1799095	chr16:46916670-46972671	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1063660	chr16:46930623-46978792	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56006015	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46919000-46963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:46928400-46966000	Strong transcription	Fetal Brain Female	brain
3	chr16:46929400-46965200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:46930800-46965400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:46930800-46968400	Weak transcription	Right Atrium	heart
6	chr16:46931600-46965200	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr16:46932200-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr16:46933600-46965400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:46933800-46965800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr16:46934000-46963400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr16:46939600-46964800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:46940000-46964600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:46943200-46965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr16:46943200-46965400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr16:46943400-46965000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr16:46943400-46965000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr16:46943400-46965200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:46943400-46965400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:46943400-46965400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:46943400-46965400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr16:46945800-46965200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:46945800-46965400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr16:46949200-46963400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr16:46949800-46964200	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr16:46950000-46965200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr16:46951800-46966800	Weak transcription	Fetal Brain Male	brain
27	chr16:46952200-46963400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr16:46953600-46963000	Strong transcription	Brain Cingulate Gyrus	brain
29	chr16:46953600-46965000	Weak transcription	A549	lung
30	chr16:46954000-46963800	Weak transcription	K562	blood
31	chr16:46954400-46963400	Weak transcription	GM12878-XiMat	blood
32	chr16:46954400-46963600	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr16:46954800-46962600	Weak transcription	Thymus	Thymus
34	chr16:46955400-46965200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr16:46955600-46962800	Strong transcription	Brain Hippocampus Middle	brain
36	chr16:46955600-46963200	Strong transcription	Placenta	Placenta
37	chr16:46955600-46964200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr16:46955600-46965200	Strong transcription	Liver	Liver
39	chr16:46955600-46966600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr16:46955800-46961800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:46955800-46965200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr16:46955800-46965800	Strong transcription	Brain Germinal Matrix	brain
43	chr16:46956000-46962600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr16:46956000-46965200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr16:46956200-46963800	Strong transcription	Lung	lung
46	chr16:46956200-46963800	Weak transcription	Small Intestine	intestine
47	chr16:46956200-46966800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr16:46956400-46961800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr16:46956400-46961800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr16:46956400-46962800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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