Variant report

Variant	rs12116738
Chromosome Location	chr1:169651770-169651771
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1011266	1.00[AFR][1000 genomes]
rs10489183	1.00[AFR][1000 genomes]
rs12133642	0.83[EUR][1000 genomes]
rs12133666	0.83[EUR][1000 genomes]
rs12133892	0.83[EUR][1000 genomes]
rs12135214	0.83[EUR][1000 genomes]
rs12135973	0.83[EUR][1000 genomes]
rs12137905	0.83[EUR][1000 genomes]
rs12142956	0.83[EUR][1000 genomes]
rs12142988	0.83[EUR][1000 genomes]
rs1569457	0.83[EUR][1000 genomes]
rs3917448	0.83[EUR][1000 genomes]
rs4987267	0.83[EUR][1000 genomes]
rs4987271	0.83[EUR][1000 genomes]
rs4987284	0.83[EUR][1000 genomes]
rs4987299	0.80[EUR][1000 genomes]
rs4987302	0.83[EUR][1000 genomes]
rs4987304	0.83[EUR][1000 genomes]
rs4987307	0.83[EUR][1000 genomes]
rs4987308	0.83[EUR][1000 genomes]
rs4987317	0.83[EUR][1000 genomes]
rs4987323	0.83[EUR][1000 genomes]
rs4987324	0.83[EUR][1000 genomes]
rs4987325	0.83[EUR][1000 genomes]
rs4987340	0.85[EUR][1000 genomes]
rs4987343	0.85[EUR][1000 genomes]
rs4987345	0.85[EUR][1000 genomes]
rs4987363	0.85[EUR][1000 genomes]
rs4987395	0.83[EUR][1000 genomes]
rs909628	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12116738	METTL18	cis	Adipose Subcutaneous	GTEx
rs12116738	METTL18	cis	lung	GTEx
rs12116738	METTL18	cis	Esophagus Muscularis	GTEx
rs12116738	METTL18	cis	Thyroid	GTEx
rs12116738	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs12116738	METTL18	cis	Artery Tibial	GTEx
rs12116738	METTL18	cis	Muscle Skeletal	GTEx
rs12116738	METTL18	cis	Heart Left Ventricle	GTEx
rs12116738	METTL18	cis	Nerve Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169645000-169652200	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr1:169646800-169651800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:169647800-169659600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr1:169647800-169660000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:169648000-169653400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:169648200-169652200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169648200-169659000	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:169648400-169652200	Enhancers	Primary T cells from cord blood	blood
9	chr1:169650000-169652000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr1:169650400-169652600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:169650600-169652400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:169650600-169653200	Enhancers	GM12878-XiMat	blood
13	chr1:169650600-169655800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr1:169650600-169656600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:169650600-169657800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:169650600-169658400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:169650800-169657000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:169651000-169652400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr1:169651200-169652000	Enhancers	Dnd41	blood
20	chr1:169651200-169653000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:169651400-169652000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr1:169651400-169652400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:169651600-169651800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr1:169651600-169652000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr1:169651600-169653000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:169651600-169656600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links