Variant report

Variant	rs7530493
Chromosome Location	chr1:220989700-220989701
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10495152	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10863567	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10863568	0.93[ASN][1000 genomes]
rs11118609	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11118611	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11118614	1.00[YRI][hapmap]
rs11118615	0.98[ASN][1000 genomes]
rs11118616	0.97[ASN][1000 genomes]
rs11118619	0.96[ASN][1000 genomes]
rs11590678	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12057411	0.97[ASN][1000 genomes]
rs12073837	0.96[ASN][1000 genomes]
rs12089958	0.97[ASN][1000 genomes]
rs12117818	0.97[ASN][1000 genomes]
rs12124030	0.86[ASN][1000 genomes]
rs12139139	0.97[ASN][1000 genomes]
rs12145674	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1335919	0.93[ASN][1000 genomes]
rs1494368	0.97[ASN][1000 genomes]
rs1494372	0.94[ASN][1000 genomes]
rs17008806	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17008835	1.00[CEU][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs17596850	0.98[ASN][1000 genomes]
rs17650107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2242358	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs2279638	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2378425	0.94[ASN][1000 genomes]
rs2642421	0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs35730037	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4143773	1.00[ASN][1000 genomes]
rs61830270	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61830289	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6541161	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6668666	0.98[ASN][1000 genomes]
rs6673877	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6693017	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530074	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7530176	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7544735	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7553447	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs881995	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs903319	0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs984676	0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7530493	IARS2	cis	cerebellum	SCAN
rs7530493	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:58 , 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	chr1:220971200-220991400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:220973200-220991800	Weak transcription	Brain Anterior Caudate	brain
4	chr1:220973400-221000200	Weak transcription	Placenta	Placenta
5	chr1:220974000-220992800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:220974200-220991200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:220975200-220992000	Weak transcription	Brain Germinal Matrix	brain
8	chr1:220975600-220991400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:220978400-220991200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:220980400-221001400	Weak transcription	Gastric	stomach
11	chr1:220981400-220991600	Strong transcription	Fetal Intestine Small	intestine
12	chr1:220984000-220991600	Weak transcription	Small Intestine	intestine
13	chr1:220984000-220992200	Weak transcription	Esophagus	oesophagus
14	chr1:220984000-220997400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:220984000-220999800	Weak transcription	Colonic Mucosa	Colon
16	chr1:220984200-220990400	Strong transcription	Adipose Nuclei	Adipose
17	chr1:220984200-220991400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:220984200-220991400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:220984200-220991400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:220984200-220991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:220984200-220991600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:220984200-220991800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:220984200-220992000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:220984200-220992200	Weak transcription	Lung	lung
25	chr1:220984200-220992400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:220984200-220993400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:220984200-221001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:220984600-220999600	Weak transcription	Left Ventricle	heart
29	chr1:220984600-221006600	Weak transcription	Psoas Muscle	Psoas
30	chr1:220984800-220991600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:220984800-220993000	Weak transcription	Right Ventricle	heart
32	chr1:220985000-220991800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:220985400-220990200	Strong transcription	Aorta	Aorta
34	chr1:220986000-220990200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:220986000-220991600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:220986400-220990400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:220986800-220991800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:220986800-220992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:220987200-220990000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:220987200-220990600	Enhancers	Rectal Smooth Muscle	rectum
41	chr1:220987200-220991600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:220987400-220990000	Enhancers	Colon Smooth Muscle	Colon
43	chr1:220987400-220997000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:220987600-220990400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:220987600-221003800	Weak transcription	HepG2	liver
46	chr1:220988000-220989800	Strong transcription	Spleen	Spleen
47	chr1:220988200-220991600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:220988400-220990000	Strong transcription	Hela-S3	cervix
49	chr1:220988400-220990200	Enhancers	Fetal Lung	lung
50	chr1:220988800-220991000	Strong transcription	Liver	Liver

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