Variant report

Variant	rs17596850
Chromosome Location	chr1:220992343-220992344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10495152	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863567	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863568	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118609	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118611	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118615	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118616	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118619	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590678	0.84[ASN][1000 genomes]
rs12057411	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12073837	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12089958	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12117818	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124030	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12129004	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12139139	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12141189	0.80[CEU][hapmap]
rs12145674	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335919	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1494368	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1494371	0.81[EUR][1000 genomes]
rs1494372	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008806	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17597773	0.80[CEU][hapmap]
rs17650107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242358	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs2279638	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378425	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2642421	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs35730037	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4143773	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61830270	0.90[ASN][1000 genomes]
rs61830289	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6541161	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668666	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673877	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693017	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7530074	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530176	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530493	0.98[ASN][1000 genomes]
rs7544735	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553447	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs881995	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903319	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs984676	0.82[EUR][1000 genomes];0.96[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
rs17596850	BPNT1	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

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	chr1:220974000-220992800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:220980400-221001400	Weak transcription	Gastric	stomach
5	chr1:220984000-220997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:220984000-220999800	Weak transcription	Colonic Mucosa	Colon
7	chr1:220984200-220992400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:220984200-220993400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:220984200-221001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:220984600-220999600	Weak transcription	Left Ventricle	heart
11	chr1:220984600-221006600	Weak transcription	Psoas Muscle	Psoas
12	chr1:220984800-220993000	Weak transcription	Right Ventricle	heart
13	chr1:220986800-220992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:220987400-220997000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:220987600-221003800	Weak transcription	HepG2	liver
16	chr1:220989800-220997800	Weak transcription	Spleen	Spleen
17	chr1:220989800-221000800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:220990000-220992600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:220990000-221001200	Weak transcription	Hela-S3	cervix
20	chr1:220990200-220998000	Weak transcription	Aorta	Aorta
21	chr1:220990400-220992800	Enhancers	Colon Smooth Muscle	Colon
22	chr1:220990400-220993400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:220991000-220993200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:220991000-220993600	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:220991000-220993800	Enhancers	Fetal Stomach	stomach
26	chr1:220991000-220997400	Weak transcription	Liver	Liver
27	chr1:220991200-220992800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:220991200-220993200	Enhancers	Adipose Nuclei	Adipose
29	chr1:220991200-220993400	Enhancers	Fetal Lung	lung
30	chr1:220991200-220993600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:220991400-220992600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:220991400-220992600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:220991400-220993200	Enhancers	Ovary	ovary
34	chr1:220991400-220993400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:220991400-220993400	Enhancers	NHLF	lung
36	chr1:220991400-220993600	Enhancers	NHDF-Ad	bronchial
37	chr1:220991600-220992400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr1:220991600-220992600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr1:220991600-220992800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:220991600-220993200	Enhancers	HSMM	muscle
41	chr1:220991600-220993400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:220991600-220993400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:220991600-220993600	Enhancers	HSMMtube	muscle
44	chr1:220991600-220995600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:220991600-221000800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:220991800-220992600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr1:220991800-220993400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:220992000-220992400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr1:220992000-220992400	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:220992000-220992400	Flanking Active TSS	Osteobl	bone

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