Variant report

Variant	rs17424899
Chromosome Location	chr1:56758246-56758247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11206765	0.81[EUR][1000 genomes]
rs12075857	0.81[EUR][1000 genomes]
rs12075995	0.81[EUR][1000 genomes]
rs12076123	0.81[EUR][1000 genomes]
rs12077346	0.81[EUR][1000 genomes]
rs12077564	0.81[EUR][1000 genomes]
rs12081440	0.81[EUR][1000 genomes]
rs12082680	0.81[EUR][1000 genomes]
rs12567619	0.81[EUR][1000 genomes]
rs17113677	0.88[AFR][1000 genomes]
rs17113689	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17424500	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17425099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17425772	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17458279	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17459027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000141	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2000142	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55633488	0.81[EUR][1000 genomes]
rs55742346	0.81[EUR][1000 genomes]
rs56022955	0.81[EUR][1000 genomes]
rs56237067	0.81[EUR][1000 genomes]
rs61379230	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72660452	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72677472	0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17424899	MYSM1	cis	cerebellum	SCAN
rs17424899	CC2D1B	cis	parietal	SCAN
rs17424899	CDCP2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56748400-56759600	Weak transcription	Aorta	Aorta
2	chr1:56753200-56763600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:56756000-56761800	Weak transcription	HepG2	liver
4	chr1:56756800-56758600	Enhancers	Psoas Muscle	Psoas
5	chr1:56756800-56758600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:56757400-56761600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:56757600-56758600	Weak transcription	HSMMtube	muscle
8	chr1:56757600-56761800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:56757800-56758800	Weak transcription	Lung	lung
10	chr1:56757800-56761600	Weak transcription	Right Atrium	heart
11	chr1:56757800-56762200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:56757800-56762600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:56757800-56762800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:56757800-56763000	Weak transcription	Fetal Heart	heart
15	chr1:56757800-56763200	Weak transcription	Fetal Intestine Large	intestine
16	chr1:56757800-56764800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:56757800-56765200	Weak transcription	Ovary	ovary
18	chr1:56757800-56786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:56758000-56759400	Weak transcription	Left Ventricle	heart
20	chr1:56758000-56763000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:56758000-56768000	Weak transcription	Right Ventricle	heart

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