Variant report

Variant	rs1323782
Chromosome Location	chr9:85878615-85878616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10512138	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10867979	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11139998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11139999	0.83[ASN][1000 genomes]
rs11140001	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140009	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs11140010	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs12003055	0.85[EUR][1000 genomes]
rs12005318	0.85[EUR][1000 genomes]
rs12336693	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12339855	0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12345712	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12376739	0.81[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1323778	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs1323785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13298532	0.81[JPT][hapmap]
rs17086124	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4395967	0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs55707933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56128787	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58579431	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559718	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7034332	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7034639	0.85[EUR][1000 genomes]
rs7034898	0.85[EUR][1000 genomes]
rs7856762	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv6586	chr9:85869828-85914812	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1323782	C9orf153	cis	cerebellum	SCAN
rs1323782	RASEF	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85854800-85890400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:85855000-85881400	Weak transcription	Adipose Nuclei	Adipose
3	chr9:85856200-85910600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr9:85866200-85913000	Weak transcription	Aorta	Aorta
5	chr9:85874800-85879200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:85876200-85880400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:85876400-85880000	Weak transcription	Left Ventricle	heart
8	chr9:85876600-85880400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:85876600-85881400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:85877200-85881400	Weak transcription	Ovary	ovary
11	chr9:85877600-85880400	Enhancers	HUVEC	blood vessel
12	chr9:85877800-85881400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:85878000-85879200	Weak transcription	Psoas Muscle	Psoas
14	chr9:85878000-85880600	Weak transcription	Right Atrium	heart
15	chr9:85878200-85878800	Flanking Active TSS	Fetal Heart	heart
16	chr9:85878200-85881200	Weak transcription	Right Ventricle	heart

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