Variant report

Variant	rs829079
Chromosome Location	chr12:21999108-21999109
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1283816	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1283817	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1283822	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1299731	1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs1643235	0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs1967534	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs1972613	0.86[AMR][1000 genomes]
rs2307024	0.82[AMR][1000 genomes]
rs4148673	0.81[TSI][hapmap]
rs4148674	0.85[MEX][hapmap];0.83[TSI][hapmap]
rs4296081	0.86[AMR][1000 genomes]
rs704175	0.81[AMR][1000 genomes]
rs704176	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs704177	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs704178	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs704180	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs704185	0.82[CEU][hapmap];0.87[AMR][1000 genomes]
rs704187	0.82[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes]
rs704189	0.80[ASW][hapmap];0.82[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes]
rs704190	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs704191	0.83[TSI][hapmap]
rs7966849	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829068	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs829069	0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs829072	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs829080	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]
rs861202	0.85[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829079	SLCO1B3	cis	cerebellum	SCAN
rs829079	ABCC9	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr12:21997600-21999200	Strong transcription	Fetal Muscle Leg	muscle
18	chr12:21997600-22016600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:21998400-22003000	Weak transcription	Left Ventricle	heart
20	chr12:21999000-22000200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:21999000-22001600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links