Variant report

Variant	rs942280
Chromosome Location	chr9:85905861-85905862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10117251	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs10118491	0.81[MEX][hapmap]
rs10780587	0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs10867967	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10867971	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867973	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867974	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10867975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10867977	0.92[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10867980	0.81[CHD][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs10867981	0.81[CHD][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs10867982	0.80[AMR][1000 genomes]
rs10867983	0.80[AMR][1000 genomes]
rs10867984	0.80[AMR][1000 genomes]
rs11140004	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11140007	0.80[AMR][1000 genomes]
rs11140011	0.80[AMR][1000 genomes]
rs11140013	0.80[AMR][1000 genomes]
rs11140015	0.80[AMR][1000 genomes]
rs11795034	0.82[ASN][1000 genomes]
rs11795096	0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1323775	0.80[CEU][hapmap];0.80[AMR][1000 genomes]
rs1323776	0.80[AMR][1000 genomes]
rs1323784	0.81[ASN][1000 genomes]
rs1359167	0.81[CHD][hapmap]
rs1359168	0.81[CHD][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs1535750	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs1535752	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535753	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1544064	0.87[CHB][hapmap]
rs1886125	0.81[MEX][hapmap]
rs2209186	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2209187	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2209188	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378658	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2889953	0.81[CHB][hapmap]
rs3739658	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4418413	0.87[EUR][1000 genomes]
rs4877751	0.82[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7039712	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7039947	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72743036	0.82[ASN][1000 genomes]
rs942278	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942279	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs942282	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942283	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs942280	C9orf153	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85856200-85910600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr9:85866200-85913000	Weak transcription	Aorta	Aorta
3	chr9:85884200-85912400	Weak transcription	HepG2	liver
4	chr9:85895000-85912800	Weak transcription	Fetal Brain Female	brain
5	chr9:85896000-85913600	Weak transcription	Psoas Muscle	Psoas
6	chr9:85896000-85919800	Weak transcription	Lung	lung
7	chr9:85896400-85912600	Weak transcription	Gastric	stomach
8	chr9:85896400-85913400	Weak transcription	Brain Germinal Matrix	brain
9	chr9:85896600-85913000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr9:85896800-85906200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:85896800-85910800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:85896800-85922800	Weak transcription	Spleen	Spleen
13	chr9:85897000-85912600	Weak transcription	Adipose Nuclei	Adipose
14	chr9:85897000-85912600	Weak transcription	Ovary	ovary
15	chr9:85897000-85912800	Weak transcription	Right Ventricle	heart
16	chr9:85897200-85912000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:85897200-85913000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:85897200-85919200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:85897200-85922000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:85897400-85914800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:85902400-85907800	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:85905400-85906000	Strong transcription	Left Ventricle	heart
23	chr9:85905600-85906000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:85905600-85906800	Enhancers	Pancreas	Pancrea
25	chr9:85905800-85919000	Weak transcription	Fetal Stomach	stomach

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