Variant report

Variant	rs9534566
Chromosome Location	chr13:47787665-47787666
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1537457	0.83[ASN][1000 genomes]
rs1819501	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1855286	0.91[ASN][1000 genomes]
rs1855288	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406095	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2406100	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142742	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4142743	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561358	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7331671	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7332153	0.81[ASN][1000 genomes]
rs7333768	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7333963	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7333999	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7338907	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7992586	0.80[AMR][1000 genomes]
rs7995117	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7996698	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	esv2763019	chr13:47348229-48123447	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3394678	chr13:47678184-48039379	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832599	chr13:47703075-47873855	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9534566	HTR2A	cis	cerebellum	SCAN
rs9534566	RCBTB1	cis	cerebellum	SCAN
rs9534566	KRT5	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:47784800-47790200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:47785000-47787800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr13:47785800-47788800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:47785800-47788800	Weak transcription	HMEC	breast
5	chr13:47785800-47790000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:47786000-47789400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr13:47786000-47789600	Weak transcription	NH-A	brain
8	chr13:47786000-47789600	Weak transcription	NHEK	skin
9	chr13:47786400-47788200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:47786600-47789600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:47786600-47790000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr13:47786800-47787800	Enhancers	HSMMtube	muscle
13	chr13:47786800-47790000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:47787000-47788000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:47787000-47789000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:47787200-47788000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr13:47787200-47789600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr13:47787600-47787800	Enhancers	HSMM	muscle
19	chr13:47787600-47788600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:47787600-47790000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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