Variant report

Variant	rs17459027
Chromosome Location	chr1:56762342-56762343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17113677	0.88[AFR][1000 genomes]
rs17113689	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17424500	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17424899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17425099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17425772	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17458279	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2000141	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2000142	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61379230	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72660452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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
rs17459027	CC2D1B	cis	parietal	SCAN
rs17459027	MYSM1	cis	cerebellum	SCAN
rs17459027	CDCP2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56753200-56763600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:56757800-56762600	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:56757800-56762800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:56757800-56763000	Weak transcription	Fetal Heart	heart
5	chr1:56757800-56763200	Weak transcription	Fetal Intestine Large	intestine
6	chr1:56757800-56764800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:56757800-56765200	Weak transcription	Ovary	ovary
8	chr1:56757800-56786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:56758000-56763000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:56758000-56768000	Weak transcription	Right Ventricle	heart
11	chr1:56758600-56770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:56759800-56767600	Weak transcription	Aorta	Aorta
13	chr1:56759800-56768000	Weak transcription	Left Ventricle	heart
14	chr1:56760200-56763400	Weak transcription	Psoas Muscle	Psoas
15	chr1:56761600-56762600	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:56761600-56762800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:56761600-56762800	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:56761600-56762800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:56761600-56762800	Enhancers	Fetal Thymus	thymus
20	chr1:56761600-56762800	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr1:56761600-56763000	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:56761600-56763000	Enhancers	Right Atrium	heart
23	chr1:56761800-56762600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:56761800-56762600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:56761800-56764000	Enhancers	Placenta	Placenta
26	chr1:56761800-56765800	Enhancers	HepG2	liver
27	chr1:56762000-56762600	Enhancers	Thymus	Thymus
28	chr1:56762000-56762600	Enhancers	GM12878-XiMat	blood
29	chr1:56762200-56766200	Enhancers	Fetal Intestine Small	intestine

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