Variant report

Variant	rs7847405
Chromosome Location	chr9:102213749-102213750
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1025901	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1025902	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10441760	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10441761	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760684	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10760685	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819666	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10819667	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10819672	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819674	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988816	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10988829	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12238127	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1360260	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1530379	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1972233	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2416768	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743345	0.85[ASN][1000 genomes]
rs4743347	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743348	0.85[ASN][1000 genomes]
rs4743349	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743353	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55750347	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57483311	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7027953	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7032399	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7032541	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7040144	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73495500	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7857445	0.85[ASN][1000 genomes]
rs7858078	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7862197	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7866560	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878449	0.85[ASN][1000 genomes]
rs880597	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831667	chr9:102068047-102285691	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv527165	chr9:102194921-102214169	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv6636	chr9:102197504-102242604	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7847405	STX17	cis	cerebellum	SCAN
rs7847405	ERP44	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102212600-102213800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:102212600-102214800	Enhancers	Fetal Heart	heart
3	chr9:102213200-102214000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:102213200-102214600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:102213400-102213800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:102213400-102213800	Enhancers	Adipose Nuclei	Adipose
7	chr9:102213400-102213800	Enhancers	Brain Hippocampus Middle	brain
8	chr9:102213400-102213800	Enhancers	Fetal Brain Male	brain
9	chr9:102213400-102213800	Enhancers	Pancreas	Pancrea
10	chr9:102213400-102213800	Enhancers	Psoas Muscle	Psoas
11	chr9:102213400-102214000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:102213400-102214000	Enhancers	Brain Angular Gyrus	brain
13	chr9:102213400-102214000	Enhancers	Brain Anterior Caudate	brain
14	chr9:102213400-102214000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:102213400-102214400	Enhancers	Fetal Brain Female	brain
16	chr9:102213400-102214400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:102213600-102213800	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr9:102213600-102213800	Bivalent Enhancer	Osteobl	bone
19	chr9:102213600-102214000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr9:102213600-102214000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:102213600-102214000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr9:102213600-102214000	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr9:102213600-102214000	Enhancers	Brain Substantia Nigra	brain
24	chr9:102213600-102214000	Enhancers	Placenta	Placenta
25	chr9:102213600-102214200	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links