Variant report

Variant	rs12120025
Chromosome Location	chr1:170066896-170066897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12116788	0.83[EUR][1000 genomes]
rs12117197	0.89[CEU][hapmap]
rs12117652	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12117699	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117892	0.80[CEU][hapmap]
rs12120229	1.00[MKK][hapmap]
rs12120443	0.80[CEU][hapmap]
rs12120968	0.83[EUR][1000 genomes]
rs12121055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12122794	1.00[EUR][1000 genomes]
rs12124561	1.00[MKK][hapmap]
rs12126443	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12128116	1.00[EUR][1000 genomes]
rs12128308	1.00[MKK][hapmap]
rs12129144	1.00[EUR][1000 genomes]
rs12130724	0.93[EUR][1000 genomes]
rs12131638	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12131740	0.80[CEU][hapmap]
rs12132173	1.00[MKK][hapmap]
rs12132530	0.83[EUR][1000 genomes]
rs12132575	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12133411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12134995	0.80[CEU][hapmap]
rs12135070	0.80[CEU][hapmap]
rs12140845	0.88[CEU][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12141501	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12141522	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12142155	1.00[EUR][1000 genomes]
rs12144057	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12144085	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12145948	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1411465	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2057249	1.00[MKK][hapmap]
rs41272485	0.83[EUR][1000 genomes]
rs4519	1.00[MKK][hapmap]
rs488488	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs511609	1.00[MKK][hapmap]
rs544008	1.00[MKK][hapmap]
rs56147946	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs565397	1.00[MKK][hapmap]
rs575147	1.00[MKK][hapmap]
rs590181	1.00[MKK][hapmap]
rs601355	1.00[MKK][hapmap]
rs629421	1.00[MKK][hapmap]
rs654664	1.00[MKK][hapmap]
rs664962	1.00[MKK][hapmap]
rs673789	1.00[MKK][hapmap]
rs688565	0.90[AMR][1000 genomes];0.83[EUR][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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv999310	chr1:170065943-170223350	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12120025	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs12120025	METTL18	cis	Esophagus Mucosa	GTEx
rs12120025	METTL18	cis	Esophagus Muscularis	GTEx
rs12120025	METTL18	cis	Thyroid	GTEx
rs12120025	C1orf156	cis	lymphoblastoid	seeQTL
rs12120025	METTL18	cis	Artery Aorta	GTEx
rs12120025	METTL18	cis	Adipose Subcutaneous	GTEx
rs12120025	MGC9084	cis	multi-tissue	Pritchard
rs12120025	METTL18	cis	Muscle Skeletal	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170064200-170067200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:170064400-170067000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:170064400-170068000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:170064600-170067200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:170064800-170067200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:170065000-170067200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:170065200-170067000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:170065400-170067400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:170065600-170068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:170065800-170067000	Enhancers	Fetal Brain Male	brain
11	chr1:170066000-170067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:170066000-170067000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:170066000-170067200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:170066200-170067400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:170066600-170067000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:170066600-170067200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:170066600-170067200	Enhancers	Fetal Kidney	kidney

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