Variant report

Variant	rs1469609
Chromosome Location	chr11:83193765-83193766
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10501540	0.85[JPT][hapmap]
rs1075718	0.88[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs10792686	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792688	0.88[CEU][hapmap]
rs10898126	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898127	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11233632	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11233641	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs11233649	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11600016	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs11601048	0.85[JPT][hapmap]
rs11606666	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs11607886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1225904	0.80[EUR][1000 genomes]
rs1225906	0.81[EUR][1000 genomes]
rs1225907	0.81[EUR][1000 genomes]
rs1228630	0.81[EUR][1000 genomes]
rs1228632	0.81[TSI][hapmap]
rs12294291	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1347008	0.82[AMR][1000 genomes]
rs1367978	0.85[JPT][hapmap]
rs1367981	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1367982	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1367984	0.87[CEU][hapmap]
rs1367985	0.88[CEU][hapmap]
rs1432043	0.82[CHB][hapmap]
rs1432052	0.83[CEU][hapmap]
rs1432053	0.88[CEU][hapmap]
rs1432054	0.88[CEU][hapmap]
rs1432058	0.91[CEU][hapmap]
rs1465671	0.88[CEU][hapmap]
rs1469610	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864774	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864775	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1897372	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009715	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2116483	0.88[CEU][hapmap]
rs2195801	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2374424	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2436152	0.88[CEU][hapmap]
rs2436157	0.81[EUR][1000 genomes]
rs2508720	0.88[CEU][hapmap]
rs2512689	0.81[EUR][1000 genomes]
rs3815986	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3815987	0.88[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs3815988	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs4341564	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4399351	0.87[CEU][hapmap]
rs4547114	0.88[CEU][hapmap]
rs473255	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs477046	0.81[TSI][hapmap]
rs478048	0.81[TSI][hapmap]
rs483020	0.87[CEU][hapmap]
rs488600	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs494071	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs500059	0.86[TSI][hapmap]
rs500359	0.88[CEU][hapmap]
rs500571	0.86[TSI][hapmap]
rs501139	0.82[CHD][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs505998	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs506718	0.87[CEU][hapmap]
rs513020	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs531531	0.88[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap]
rs533209	0.88[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap]
rs535809	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs553935	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs558426	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs575952	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs579420	0.84[CEU][hapmap]
rs581178	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs582207	0.85[CEU][hapmap]
rs583944	0.84[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs585240	0.83[CEU][hapmap]
rs590014	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs598934	0.87[CEU][hapmap]
rs600570	0.88[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap]
rs601826	0.88[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap]
rs603174	0.87[CEU][hapmap]
rs605303	0.87[CEU][hapmap]
rs605825	0.91[CEU][hapmap]
rs611766	0.84[CEU][hapmap]
rs630105	0.86[CEU][hapmap]
rs631277	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs633191	0.87[CEU][hapmap]
rs641838	0.87[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs6592116	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592117	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592119	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6592123	0.88[CEU][hapmap]
rs6592124	0.83[CEU][hapmap]
rs661927	0.87[CEU][hapmap]
rs662966	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs663399	0.88[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs667730	0.87[CEU][hapmap]
rs671321	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs684857	0.86[TSI][hapmap]
rs694613	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs7131385	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7927629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7930252	0.88[CEU][hapmap]
rs7948931	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919667	0.88[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs958246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1469609	CCDC90B	cis	cerebellum	SCAN
rs1469609	CCDC90B	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83187200-83196600	Weak transcription	Brain Substantia Nigra	brain
2	chr11:83191600-83193800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:83191600-83194000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:83191800-83195800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:83192200-83194000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:83192200-83195000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:83192200-83196800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:83192400-83195000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:83192400-83196000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:83192800-83194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:83192800-83195000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:83192800-83195000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:83192800-83195000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:83192800-83195200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:83192800-83196400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:83192800-83197400	Weak transcription	Brain Angular Gyrus	brain
17	chr11:83192800-83211200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:83193000-83195000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:83193000-83197600	Weak transcription	Brain Anterior Caudate	brain
20	chr11:83193200-83194000	Enhancers	Pancreatic Islets	Pancreatic Islet

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