Variant report

Variant	rs9480490
Chromosome Location	chr6:150926271-150926272
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11968779	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1352975	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs17080012	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs201531	0.82[EUR][1000 genomes]
rs2345668	0.80[ASN][1000 genomes]
rs2345669	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs275348	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4323318	0.90[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4400227	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4530869	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs4869921	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869922	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869924	1.00[JPT][hapmap]
rs4869932	1.00[JPT][hapmap]
rs4870533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870534	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[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870535	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4870537	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432653	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432656	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432657	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432658	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62432659	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434060	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434061	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434062	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434064	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62434092	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434093	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434094	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434095	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434096	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434097	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434098	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434099	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434100	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434101	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434102	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62434103	0.86[EUR][1000 genomes]
rs62434104	0.86[EUR][1000 genomes]
rs73002187	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73002188	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73002195	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73004311	0.85[EUR][1000 genomes]
rs73016045	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73016054	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9478767	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478768	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478769	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478770	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478771	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9478772	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9478773	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9478774	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9478777	1.00[JPT][hapmap]
rs9480492	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9480493	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480494	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480495	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480496	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480497	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480499	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9480503	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9480505	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9480511	1.00[JPT][hapmap]
rs9480516	1.00[JPT][hapmap]
rs9480517	1.00[JPT][hapmap]
rs9480518	1.00[JPT][hapmap]
rs9480521	1.00[JPT][hapmap]
rs9480522	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv437526	chr6:150923115-150926499	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
3	nsv464080	chr6:150923115-150941310	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv604851	chr6:150923115-150941310	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9480490	IYD	cis	cerebellum	SCAN
rs9480490	RAET1E	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150922200-150927600	Weak transcription	Spleen	Spleen
2	chr6:150922200-150930600	Weak transcription	Aorta	Aorta
3	chr6:150922400-150927600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:150922400-150927600	Weak transcription	Brain Substantia Nigra	brain
5	chr6:150922400-150927600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:150922400-150941400	Weak transcription	Colonic Mucosa	Colon
7	chr6:150922600-150927800	Weak transcription	Small Intestine	intestine
8	chr6:150922600-150928000	Weak transcription	Liver	Liver
9	chr6:150922800-150927600	Weak transcription	Brain Angular Gyrus	brain
10	chr6:150922800-150929600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:150923000-150927000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:150923000-150927200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:150923000-150927200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:150923000-150927400	Weak transcription	Placenta	Placenta
15	chr6:150923000-150927400	Weak transcription	Right Atrium	heart
16	chr6:150923000-150927400	Weak transcription	HMEC	breast
17	chr6:150923000-150927600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:150923000-150938600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:150923600-150926800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:150923600-150930800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:150924800-150926600	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr6:150924800-150929200	Enhancers	Fetal Kidney	kidney
23	chr6:150925600-150927400	Strong transcription	Primary B cells from cord blood	blood
24	chr6:150925600-150929400	Enhancers	Thymus	Thymus
25	chr6:150925600-150931600	Genic enhancers	Fetal Thymus	thymus

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