Variant report

Variant	rs12719759
Chromosome Location	chr16:46991439-46991440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:46989483..46991603-chr16:46991915..46995032,3	K562	blood:
2	chr16:46990119..46993112-chr16:47006467..47008699,2	MCF-7	breast:
3	chr16:46989650..46991620-chr16:47006185..47008224,2	MCF-7	breast:
4	chr16:46987939..46992343-chr16:46992446..46995996,5	K562	blood:
5	chr16:46989086..46991933-chr16:47005435..47007700,2	K562	blood:

Variant related genes	Relation type
ENSG00000069345	Chromatin interaction
ENSG00000261173	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10459877	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11247542	0.83[EUR][1000 genomes]
rs11859515	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12445492	0.81[EUR][1000 genomes]
rs12447719	0.83[EUR][1000 genomes]
rs12596824	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12925296	0.83[EUR][1000 genomes]
rs1362406	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1376734	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1551188	0.83[EUR][1000 genomes]
rs1894886	0.81[EUR][1000 genomes]
rs1978336	0.83[EUR][1000 genomes]
rs2058673	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2341648	0.88[EUR][1000 genomes]
rs35405784	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4577108	0.83[EUR][1000 genomes]
rs4966781	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4966794	0.85[EUR][1000 genomes]
rs4966795	0.85[EUR][1000 genomes]
rs4966800	0.83[EUR][1000 genomes]
rs4967664	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4967696	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4967724	0.84[AFR][1000 genomes]
rs4967739	0.81[EUR][1000 genomes]
rs7189628	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7199379	0.83[EUR][1000 genomes]
rs7199772	0.85[EUR][1000 genomes]
rs7202325	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7203206	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8046142	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8047353	0.83[EUR][1000 genomes]
rs8052160	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8054039	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8058144	0.89[AFR][1000 genomes]
rs8060193	0.81[EUR][1000 genomes]
rs9745921	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9925290	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9925525	0.88[AMR][1000 genomes]
rs9927843	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12719759	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46964200-46991800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr16:46970400-46999000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:46977600-47006200	Weak transcription	Stomach Mucosa	stomach
4	chr16:46983800-46996200	Weak transcription	Small Intestine	intestine
5	chr16:46987000-46993600	Weak transcription	Fetal Brain Male	brain
6	chr16:46987000-46995600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr16:46987400-46995400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr16:46987600-47003400	Strong transcription	Liver	Liver
9	chr16:46988000-46991800	Strong transcription	HepG2	liver
10	chr16:46988000-46994000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:46988000-46994200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:46988000-46994200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr16:46988000-46994400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr16:46988000-46994600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr16:46988000-46994600	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr16:46988000-46994600	Strong transcription	A549	lung
17	chr16:46988000-46995000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr16:46988000-46995400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:46988000-46995400	Strong transcription	GM12878-XiMat	blood
20	chr16:46988000-46995600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr16:46988000-46995600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr16:46988000-46995600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:46988000-46995600	Strong transcription	Adipose Nuclei	Adipose
24	chr16:46988000-46995800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr16:46988000-46996000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr16:46988000-46996200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:46988000-47002800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr16:46988000-47003000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr16:46988000-47003200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:46988000-47003200	Strong transcription	Brain Germinal Matrix	brain
31	chr16:46988000-47004200	Strong transcription	Fetal Thymus	thymus
32	chr16:46988000-47004400	Strong transcription	Primary T cells from cord blood	blood
33	chr16:46988000-47005400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr16:46988000-47005400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr16:46988000-47005600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:46988000-47005800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr16:46988200-46994200	Strong transcription	Brain Anterior Caudate	brain
38	chr16:46988200-46995600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:46988200-47005400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr16:46988400-46993200	Weak transcription	Fetal Heart	heart
41	chr16:46988400-46993600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr16:46988400-46994400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:46988400-46994400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr16:46988400-46994400	Strong transcription	Brain Substantia Nigra	brain
45	chr16:46988400-46994600	Strong transcription	HSMM	muscle
46	chr16:46988400-46994600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr16:46988400-46995000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr16:46988400-46995000	Strong transcription	Primary B cells from cord blood	blood
49	chr16:46988400-46995200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr16:46988400-46995400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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