Variant report

Variant	rs829080
Chromosome Location	chr12:21999863-21999864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1283816	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap]
rs1283817	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1283822	0.86[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1299731	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1967534	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs704176	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs704177	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs704178	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs704180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs704182	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7966849	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs829068	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs829069	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs829072	0.81[ASN][1000 genomes]
rs829079	0.93[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[ASN][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	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv470275	chr12:21938544-22126314	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs829080	SLCO1B3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21958400-22003000	Weak transcription	Psoas Muscle	Psoas
2	chr12:21973800-22025400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:21980600-22002800	Weak transcription	Fetal Heart	heart
4	chr12:21983600-22002800	Strong transcription	Liver	Liver
5	chr12:21983800-22002000	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:21983800-22003000	Weak transcription	Pancreas	Pancrea
7	chr12:21985000-22003000	Weak transcription	Right Ventricle	heart
8	chr12:21985400-22005000	Weak transcription	NHLF	lung
9	chr12:21985600-22002800	Weak transcription	Fetal Lung	lung
10	chr12:21985800-22004800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:21995400-22003200	Weak transcription	Adipose Nuclei	Adipose
12	chr12:21995600-22004400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:21995600-22022200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:21995600-22034800	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:21995800-22022600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:21997400-22000000	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:21997600-22016600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:21998400-22003000	Weak transcription	Left Ventricle	heart
19	chr12:21999000-22000200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:21999000-22001600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:21999200-22015400	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:21999800-22003600	Enhancers	Pancreatic Islets	Pancreatic Islet

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