Variant report

Variant	rs2009715
Chromosome Location	chr11:83211686-83211687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:83210116..83211836-chr20:60641731..60644214,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10501540	0.81[JPT][hapmap]
rs10751093	0.85[JPT][hapmap]
rs1075718	0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs10792686	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792688	0.88[CEU][hapmap]
rs10898126	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898127	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898129	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11233632	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11233641	0.84[JPT][hapmap]
rs11233649	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233654	0.85[JPT][hapmap]
rs11233657	0.85[JPT][hapmap]
rs11600016	0.81[JPT][hapmap]
rs11601048	0.81[JPT][hapmap]
rs11606666	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs11607886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12223102	0.85[JPT][hapmap]
rs1228632	0.85[TSI][hapmap]
rs12294291	1.00[CEU][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12794550	0.85[JPT][hapmap]
rs1347008	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1367978	0.81[JPT][hapmap]
rs1367981	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367982	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1367984	0.87[CEU][hapmap]
rs1367985	0.88[CEU][hapmap]
rs1432043	0.85[JPT][hapmap]
rs1432044	0.85[JPT][hapmap]
rs1432049	0.85[JPT][hapmap]
rs1432052	0.82[CEU][hapmap]
rs1432053	0.88[CEU][hapmap]
rs1432054	0.88[CEU][hapmap]
rs1432058	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1465671	0.88[CEU][hapmap]
rs1469609	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]
rs1469610	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864774	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864775	0.81[JPT][hapmap]
rs1897372	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2116483	0.88[CEU][hapmap]
rs2195801	0.92[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2374424	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2436152	0.87[CEU][hapmap]
rs2508720	0.87[CEU][hapmap]
rs3815986	0.96[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3815987	0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3815988	0.92[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4341564	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4399351	0.87[CEU][hapmap]
rs4547114	0.88[CEU][hapmap]
rs473255	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs477046	0.85[TSI][hapmap]
rs478048	0.85[TSI][hapmap]
rs483020	0.87[CEU][hapmap]
rs488600	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs494071	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs500059	0.90[TSI][hapmap]
rs500359	0.87[CEU][hapmap]
rs500571	0.90[TSI][hapmap]
rs501139	0.84[CHD][hapmap];0.83[MEX][hapmap]
rs505998	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs506718	0.87[CEU][hapmap]
rs513020	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs531531	0.87[CEU][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap]
rs533209	0.87[CEU][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap]
rs535809	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs553935	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs558426	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs575952	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs579420	0.83[CEU][hapmap]
rs581178	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs582207	0.85[CEU][hapmap]
rs583944	0.83[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs585240	0.83[CEU][hapmap]
rs590014	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs598934	0.87[CEU][hapmap]
rs600570	0.87[CEU][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap]
rs601826	0.87[CEU][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap]
rs603174	0.87[CEU][hapmap]
rs605303	0.87[CEU][hapmap]
rs605825	0.91[CEU][hapmap]
rs611766	0.83[CEU][hapmap]
rs630105	0.86[CEU][hapmap]
rs631277	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs633191	0.87[CEU][hapmap]
rs641838	0.87[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs6592116	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6592117	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6592119	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6592123	0.88[CEU][hapmap]
rs6592124	0.82[CEU][hapmap]
rs661927	0.87[CEU][hapmap]
rs662966	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs663399	0.87[CEU][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap]
rs666845	0.83[TSI][hapmap]
rs667730	0.87[CEU][hapmap]
rs671321	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs684857	0.90[TSI][hapmap]
rs694613	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs7122339	0.81[EUR][1000 genomes]
rs7127319	0.85[JPT][hapmap]
rs7127859	0.85[JPT][hapmap]
rs7131385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7927629	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7930252	0.88[CEU][hapmap]
rs7948931	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919667	0.87[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs958246	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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	esv3333958	chr11:83210104-83212052	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2009715	CCDC90B	cis	cerebellum	SCAN
rs2009715	CCDC90B	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83211400-83220000	Weak transcription	Brain Angular Gyrus	brain
2	chr11:83211600-83213400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:83211600-83215200	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:83211600-83219000	Weak transcription	Brain Substantia Nigra	brain
5	chr11:83211600-83222200	Weak transcription	Brain Inferior Temporal Lobe	brain

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