Variant report

Variant	rs1566602
Chromosome Location	chr1:211191060-211191061
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	chr1:211079490..211081106-chr1:211190726..211193541,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10779548	0.81[CEU][hapmap]
rs10863871	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119636	0.88[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11119639	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1354112	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs1393029	0.81[CEU][hapmap]
rs1501553	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501561	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1542887	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1546277	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1587579	0.82[AFR][1000 genomes]
rs1777242	0.86[CEU][hapmap];0.82[YRI][hapmap]
rs1846946	0.81[CEU][hapmap]
rs1875437	0.81[CEU][hapmap]
rs2062673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2088877	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2102129	0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202095	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2358092	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2358114	0.82[AMR][1000 genomes]
rs2358115	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2358117	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4639824	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951491	0.86[CEU][hapmap]
rs4951700	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4951701	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951702	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4951704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs4951706	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4951708	0.95[AFR][1000 genomes]
rs6686447	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6692020	0.81[CEU][hapmap]
rs6702809	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7415388	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7543777	0.80[AMR][1000 genomes]
rs924567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924568	1.00[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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973945	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs985382	0.88[ASW][hapmap];0.81[CEU][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1566602	CD46	cis	cerebellum	SCAN
rs1566602	SERTAD4	cis	cerebellum	SCAN
rs1566602	PLXNA2	cis	parietal	SCAN
rs1566602	NSL1	cis	parietal	SCAN
rs1566602	C1orf74	cis	parietal	SCAN
rs1566602	IKBKE	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211181800-211193800	Weak transcription	Brain Anterior Caudate	brain
2	chr1:211182800-211228600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:211184800-211198600	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:211185200-211194000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:211185400-211191800	Weak transcription	HSMMtube	muscle
6	chr1:211187000-211198200	Weak transcription	Brain Angular Gyrus	brain
7	chr1:211187200-211191800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:211187400-211191800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:211187600-211198200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:211189200-211193000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:211189600-211191800	Weak transcription	HSMM	muscle
12	chr1:211190200-211191800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:211190600-211191400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:211190600-211191600	Enhancers	Hela-S3	cervix
15	chr1:211190600-211192000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:211190600-211198800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:211190800-211191800	Weak transcription	A549	lung
18	chr1:211191000-211192400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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