Variant report

Variant	rs4148665
Chromosome Location	chr12:22035247-22035248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:22034102..22036993-chr12:22040454..22043984,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10841904	0.83[ASN][1000 genomes]
rs12304313	0.93[YRI][hapmap]
rs1283798	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1283802	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1283807	0.94[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs1352909	0.94[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs1356368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292772	0.85[YRI][hapmap]
rs4148664	0.84[LWK][hapmap];0.96[YRI][hapmap]
rs4148667	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs697252	0.80[JPT][hapmap]
rs704193	0.81[JPT][hapmap]
rs704194	0.81[JPT][hapmap]
rs704206	0.94[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs704208	0.81[EUR][1000 genomes]
rs704209	0.94[CEU][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs704210	0.81[EUR][1000 genomes]
rs704212	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs704215	0.81[YRI][hapmap]
rs7137730	0.85[YRI][hapmap]
rs7301876	0.93[YRI][hapmap]
rs7308718	0.85[YRI][hapmap]
rs7958833	0.83[ASN][1000 genomes]
rs829066	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	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
rs4148665	SOX5	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22024800-22037000	Weak transcription	Left Ventricle	heart
2	chr12:22024800-22044000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:22024800-22044800	Weak transcription	Aorta	Aorta
4	chr12:22027000-22041000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:22027600-22046200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:22029400-22040800	Weak transcription	Fetal Lung	lung
7	chr12:22030600-22044800	Weak transcription	Right Ventricle	heart
8	chr12:22031600-22039400	Enhancers	Liver	Liver
9	chr12:22033600-22036200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr12:22033600-22038400	Enhancers	Fetal Heart	heart
11	chr12:22033800-22037800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:22034200-22036400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:22034800-22035400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr12:22034800-22035400	Enhancers	Stomach Smooth Muscle	stomach
15	chr12:22034800-22035600	Enhancers	Colon Smooth Muscle	Colon
16	chr12:22034800-22035800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:22034800-22035800	Enhancers	Fetal Stomach	stomach
18	chr12:22035000-22036200	Weak transcription	Right Atrium	heart
19	chr12:22035200-22036000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:22035200-22036200	Enhancers	Rectal Smooth Muscle	rectum
21	chr12:22035200-22044400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:22035200-22044800	Weak transcription	Psoas Muscle	Psoas
23	chr12:22035200-22058600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:22035200-22092200	Weak transcription	Fetal Muscle Leg	muscle

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