Variant report

Variant	rs504273
Chromosome Location	chr13:76310850-76310851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1092601	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108412	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1323710	0.81[EUR][1000 genomes]
rs1323712	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1408060	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1535730	0.89[ASN][1000 genomes]
rs1830760	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1924214	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2025354	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2328953	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328954	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2328956	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2761398	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34545980	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479824	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs480929	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4885345	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502171	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs508596	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs528783	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs560069	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs562940	0.85[EUR][1000 genomes]
rs585233	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs603274	0.83[EUR][1000 genomes]
rs607095	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs626182	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs634729	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs636505	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs636580	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7320216	0.84[CEU][hapmap]
rs7331527	0.81[CEU][hapmap]
rs7336908	0.89[ASN][1000 genomes]
rs776527	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986141	0.88[ASN][1000 genomes]
rs7991448	0.85[CEU][hapmap]
rs8002635	0.88[ASN][1000 genomes]
rs9530463	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9544028	0.88[ASN][1000 genomes]
rs9544029	0.90[ASN][1000 genomes]
rs9544034	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9544035	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9565195	0.85[EUR][1000 genomes]
rs9573627	0.88[ASN][1000 genomes]
rs9573636	0.80[AMR][1000 genomes]
rs9573647	0.84[AMR][1000 genomes];0.90[EUR][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	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1091	chr13:76282392-76327906	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs504273	TBC1D4	cis	cerebellum	SCAN
rs504273	KCTD12	cis	cerebellum	SCAN
rs504273	COMMD6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76294800-76321800	Weak transcription	NH-A	brain
2	chr13:76298600-76313000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:76298600-76318800	Weak transcription	Gastric	stomach
4	chr13:76299800-76313000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr13:76300200-76313000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:76306200-76330600	Weak transcription	Thymus	Thymus
7	chr13:76307200-76318200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:76307800-76312400	Strong transcription	HSMM	muscle
9	chr13:76308200-76314800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:76308200-76324800	Weak transcription	Left Ventricle	heart
11	chr13:76308200-76345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:76308400-76313200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:76308600-76312800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:76309000-76311000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:76309200-76311000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:76309200-76311400	Enhancers	NHDF-Ad	bronchial
17	chr13:76309200-76314200	Weak transcription	Right Atrium	heart
18	chr13:76309600-76315000	Genic enhancers	Osteobl	bone
19	chr13:76310000-76311000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:76310200-76311000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr13:76310200-76313200	Genic enhancers	Muscle Satellite Cultured Cells	--
22	chr13:76310200-76316000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:76310400-76311000	Enhancers	Aorta	Aorta
24	chr13:76310400-76311000	Enhancers	Fetal Lung	lung
25	chr13:76310400-76311000	Enhancers	Fetal Muscle Leg	muscle
26	chr13:76310400-76311200	Enhancers	NHLF	lung
27	chr13:76310400-76313400	Enhancers	HSMMtube	muscle
28	chr13:76310800-76311000	Enhancers	Fetal Kidney	kidney
29	chr13:76310800-76311000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr13:76310800-76312800	Weak transcription	HepG2	liver

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