Variant report

Variant	rs12402181
Chromosome Location	chr1:67094171-67094172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

miRNA name	Chromosome Location	mirBase accession
hsa-miR-3117-3p	chr1:67094168-67094188	MIMAT0014979

Variant related genes	Relation type
ZFYVE19	Mature miRNA region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493411	0.89[EUR][1000 genomes]
rs10789211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889638	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11208910	0.93[EUR][1000 genomes]
rs11208916	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11208924	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11208929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021913	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12023176	0.89[ASN][1000 genomes]
rs12034344	0.93[EUR][1000 genomes]
rs12039282	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041930	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046520	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12093843	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12565798	0.87[EUR][1000 genomes]
rs12567556	0.93[EUR][1000 genomes]
rs1925342	0.83[AMR][1000 genomes]
rs2312153	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795531	0.91[EUR][1000 genomes]
rs6588209	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6588214	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6701907	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6701988	0.93[EUR][1000 genomes]
rs72918447	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512692	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519639	0.89[EUR][1000 genomes]
rs7526812	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7535076	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7551301	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12402181	SGIP1	cis	Whole Blood	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67071600-67094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:67084200-67099800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
5	chr1:67090800-67094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:67090800-67099600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:67090800-67108400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:67091000-67099000	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:67091200-67100800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:67091200-67100800	Weak transcription	NHLF	lung
11	chr1:67091200-67107400	Weak transcription	NHDF-Ad	bronchial
12	chr1:67091200-67108600	Weak transcription	Osteobl	bone
13	chr1:67091200-67108800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:67091200-67128000	Weak transcription	NH-A	brain
15	chr1:67091400-67098200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:67091400-67105200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:67091400-67107400	Weak transcription	Fetal Brain Female	brain
18	chr1:67092000-67117200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:67092200-67099800	Weak transcription	Psoas Muscle	Psoas
20	chr1:67092200-67114200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:67092600-67095400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:67093200-67095400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:67093200-67096200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:67093200-67099000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:67093200-67100800	Weak transcription	Aorta	Aorta
26	chr1:67093200-67107800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:67094000-67095200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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