Variant report

Variant	rs1352909
Chromosome Location	chr12:22040041-22040042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1283798	0.81[JPT][hapmap]
rs1283802	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1283807	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356368	0.94[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1356369	0.94[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs4148665	0.94[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs4148667	0.89[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs704206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704208	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704210	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs704211	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs704212	0.94[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][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	nsv898899	chr12:22024093-22044210	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1352909	SOX5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22024800-22044000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:22024800-22044800	Weak transcription	Aorta	Aorta
3	chr12:22027000-22041000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:22027600-22046200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:22029400-22040800	Weak transcription	Fetal Lung	lung
6	chr12:22030600-22044800	Weak transcription	Right Ventricle	heart
7	chr12:22035200-22044400	Weak transcription	Adipose Nuclei	Adipose
8	chr12:22035200-22044800	Weak transcription	Psoas Muscle	Psoas
9	chr12:22035200-22058600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:22035200-22092200	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:22035400-22040800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:22035400-22041200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:22036200-22041000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:22036200-22041200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:22036400-22044800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:22036400-22044800	Weak transcription	Right Atrium	heart
17	chr12:22038000-22044000	Weak transcription	Fetal Stomach	stomach
18	chr12:22038400-22040200	Strong transcription	Left Ventricle	heart
19	chr12:22038400-22044600	Weak transcription	Fetal Heart	heart
20	chr12:22039600-22040200	Enhancers	Colon Smooth Muscle	Colon
21	chr12:22039600-22040800	Strong transcription	Liver	Liver
22	chr12:22039800-22041600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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