Variant report

Variant	rs12116788
Chromosome Location	chr1:170134602-170134603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12116611	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12117652	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12117699	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12120025	0.83[EUR][1000 genomes]
rs12120968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12121055	0.83[EUR][1000 genomes]
rs12122794	0.83[EUR][1000 genomes]
rs12126443	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12126954	0.95[EUR][1000 genomes]
rs12128116	0.83[EUR][1000 genomes]
rs12129144	0.83[EUR][1000 genomes]
rs12130116	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12131638	0.88[CEU][hapmap]
rs12132179	0.95[EUR][1000 genomes]
rs12132530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12132575	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12133411	0.83[EUR][1000 genomes]
rs12135203	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12135815	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12140845	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12141501	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12141965	0.95[EUR][1000 genomes]
rs12142155	0.83[EUR][1000 genomes]
rs12144057	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12144085	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12145948	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1411465	0.83[EUR][1000 genomes]
rs2150114	0.95[EUR][1000 genomes]
rs2421112	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41272485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs534412	0.95[EUR][1000 genomes]
rs56147946	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs688565	0.89[AMR][1000 genomes];0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12116788	MGC9084	cis	multi-tissue	Pritchard
rs12116788	C1orf156	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170126200-170135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:170132000-170135800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:170132200-170136600	Weak transcription	Ovary	ovary
4	chr1:170132200-170136800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:170132400-170136600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:170132400-170136600	Weak transcription	Left Ventricle	heart
7	chr1:170132400-170136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:170132400-170140200	Weak transcription	Right Ventricle	heart
9	chr1:170132600-170136800	Weak transcription	Fetal Kidney	kidney
10	chr1:170132600-170136800	Weak transcription	HSMM	muscle
11	chr1:170132600-170137200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:170132600-170137200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:170132600-170137200	Weak transcription	Osteobl	bone
14	chr1:170132600-170137600	Weak transcription	HSMMtube	muscle
15	chr1:170132800-170140600	Weak transcription	Fetal Heart	heart
16	chr1:170133200-170136800	Weak transcription	NHDF-Ad	bronchial

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