Variant report

Variant	rs12005369
Chromosome Location	chr9:86039436-86039437
allele	A/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:15)

rs_ID	r²[population]
rs11792493	1.00[ASN][1000 genomes]
rs3860915	1.00[ASN][1000 genomes]
rs55938439	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56658338	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60152061	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60329197	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745036	1.00[ASN][1000 genomes]
rs72745047	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745060	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745080	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745084	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745087	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745090	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745099	0.89[EUR][1000 genomes];1.00[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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12005369	SLC28A3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86013400-86041000	Weak transcription	Aorta	Aorta
2	chr9:86021200-86041600	Weak transcription	Right Ventricle	heart
3	chr9:86035400-86041400	Weak transcription	Psoas Muscle	Psoas
4	chr9:86036800-86041200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:86037600-86041000	Weak transcription	Adipose Nuclei	Adipose
6	chr9:86037800-86047200	Weak transcription	Fetal Stomach	stomach
7	chr9:86038000-86041400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:86038200-86040400	Enhancers	Pancreas	Pancrea
9	chr9:86038400-86045800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:86038400-86046600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:86038600-86040400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr9:86038600-86041400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:86038800-86040000	Enhancers	Fetal Lung	lung
14	chr9:86038800-86040400	Enhancers	Fetal Intestine Large	intestine
15	chr9:86039000-86040000	Enhancers	Fetal Heart	heart
16	chr9:86039200-86039600	Flanking Active TSS	HepG2	liver
17	chr9:86039200-86040200	Weak transcription	Left Ventricle	heart
18	chr9:86039200-86041200	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:86039200-86041200	Weak transcription	Gastric	stomach
20	chr9:86039200-86041200	Weak transcription	Right Atrium	heart
21	chr9:86039200-86041400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:86039200-86050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:86039400-86039600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr9:86039400-86039800	Weak transcription	Small Intestine	intestine
25	chr9:86039400-86041000	Weak transcription	Ovary	ovary

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