Variant report

Variant	rs4148674
Chromosome Location	chr12:22003544-22003545
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10841900	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11046212	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11046213	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11046215	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12825295	0.85[ASN][1000 genomes]
rs1283822	0.85[MEX][hapmap];0.83[TSI][hapmap]
rs1643235	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1972613	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2098574	0.89[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs2112080	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs2161063	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307024	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3782667	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4148673	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4296081	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs704175	0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs704185	0.88[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs704187	0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs704189	0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs704190	0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs704191	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs704192	0.85[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7966849	0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs829079	0.85[MEX][hapmap];0.83[TSI][hapmap]
rs861202	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs864360	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv1847099	chr12:22003544-22035425	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4148674	RECQL	cis	cerebellum	SCAN
rs4148674	ABCC9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21973800-22025400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:21985400-22005000	Weak transcription	NHLF	lung
3	chr12:21985800-22004800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:21995600-22004400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:21995600-22022200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:21995600-22034800	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:21995800-22022600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:21997600-22016600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:21999200-22015400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:21999800-22003600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr12:22001400-22011400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:22002800-22003600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:22002800-22003800	Enhancers	Fetal Lung	lung
14	chr12:22002800-22004000	Genic enhancers	Liver	Liver
15	chr12:22002800-22004000	Enhancers	Fetal Heart	heart
16	chr12:22003000-22003800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:22003200-22003600	Enhancers	Adipose Nuclei	Adipose
18	chr12:22003200-22004000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:22003400-22008600	Weak transcription	Pancreas	Pancrea
20	chr12:22003400-22014200	Weak transcription	Left Ventricle	heart
21	chr12:22003400-22015800	Weak transcription	Right Ventricle	heart
22	chr12:22003400-22026600	Weak transcription	Psoas Muscle	Psoas

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