Variant report

Variant	rs2792783
Chromosome Location	chr1:56754537-56754538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10789017	0.88[EUR][1000 genomes]
rs2096086	0.88[EUR][1000 genomes]
rs2777758	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2792774	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2792775	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2792776	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2793663	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2793665	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2793666	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2793672	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793675	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793677	0.81[EUR][1000 genomes]
rs2793681	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793683	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793684	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793688	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793690	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2793691	0.80[EUR][1000 genomes]
rs9436537	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9436538	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9436999	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs947252	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9787032	0.82[EUR][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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2792783	TTC4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56745400-56757000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:56748400-56759600	Weak transcription	Aorta	Aorta
3	chr1:56751200-56756000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:56751400-56756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:56751400-56757600	Weak transcription	Pancreas	Pancrea
6	chr1:56751800-56756800	Weak transcription	Lung	lung
7	chr1:56752000-56756800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:56752000-56757000	Weak transcription	Fetal Stomach	stomach
9	chr1:56752000-56757000	Weak transcription	HSMMtube	muscle
10	chr1:56752600-56756800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:56752800-56755000	Weak transcription	Left Ventricle	heart
12	chr1:56752800-56756800	Weak transcription	Adipose Nuclei	Adipose
13	chr1:56752800-56756800	Weak transcription	Psoas Muscle	Psoas
14	chr1:56752800-56756800	Weak transcription	Right Atrium	heart
15	chr1:56752800-56756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:56753200-56756800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:56753200-56763600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:56753400-56756800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:56753600-56756000	Enhancers	HepG2	liver
20	chr1:56753600-56756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:56753600-56756800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:56753600-56756800	Weak transcription	Placenta	Placenta
23	chr1:56753600-56757000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:56754200-56755200	Enhancers	Skeletal Muscle Female	skeletal muscle

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