Variant report

Variant	rs17596947
Chromosome Location	chr1:220993464-220993465
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1335920	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17649913	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs1874124	1.00[ASN][1000 genomes]
rs2642417	0.88[ASN][1000 genomes]
rs2642420	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2642422	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34404525	1.00[ASN][1000 genomes]
rs34621709	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6541160	1.00[CHB][hapmap];0.97[GIH][hapmap]
rs66488325	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549963	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1008867	chr1:220986965-220999703	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17596947	PCDHB14	trans	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220966400-220996000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:220973400-221000200	Weak transcription	Placenta	Placenta
3	chr1:220980400-221001400	Weak transcription	Gastric	stomach
4	chr1:220984000-220997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:220984000-220999800	Weak transcription	Colonic Mucosa	Colon
6	chr1:220984200-221001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:220984600-220999600	Weak transcription	Left Ventricle	heart
8	chr1:220984600-221006600	Weak transcription	Psoas Muscle	Psoas
9	chr1:220987400-220997000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:220987600-221003800	Weak transcription	HepG2	liver
11	chr1:220989800-220997800	Weak transcription	Spleen	Spleen
12	chr1:220989800-221000800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:220990000-221001200	Weak transcription	Hela-S3	cervix
14	chr1:220990200-220998000	Weak transcription	Aorta	Aorta
15	chr1:220991000-220993600	Enhancers	Rectal Smooth Muscle	rectum
16	chr1:220991000-220993800	Enhancers	Fetal Stomach	stomach
17	chr1:220991000-220997400	Weak transcription	Liver	Liver
18	chr1:220991200-220993600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:220991400-220993600	Enhancers	NHDF-Ad	bronchial
20	chr1:220991600-220993600	Enhancers	HSMMtube	muscle
21	chr1:220991600-220995600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:220991600-221000800	Weak transcription	Fetal Intestine Small	intestine
23	chr1:220992000-220997600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:220992000-220999200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:220992000-221002600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:220992200-220993600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:220992800-221001200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:220993000-220993600	Enhancers	Colon Smooth Muscle	Colon
29	chr1:220993000-220996800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:220993200-220994200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:220993200-220999200	Weak transcription	Adipose Nuclei	Adipose
32	chr1:220993200-221000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:220993200-221001000	Weak transcription	Ovary	ovary
34	chr1:220993400-220994800	Weak transcription	NHLF	lung
35	chr1:220993400-220997000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:220993400-220997200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:220993400-220997200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:220993400-221001000	Weak transcription	Primary monocytes fromperipheralblood	blood

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