Variant report

Variant	rs17070580
Chromosome Location	chr6:109738714-109738715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10080429	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040284	0.92[EUR][1000 genomes]
rs10457190	0.91[EUR][1000 genomes]
rs1048203	0.95[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs1074765	0.83[MKK][hapmap]
rs1074766	0.84[MKK][hapmap]
rs10782161	0.95[EUR][1000 genomes]
rs10782162	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs10872032	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10872034	0.82[EUR][1000 genomes]
rs11153171	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11153174	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11153175	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11153176	0.92[EUR][1000 genomes]
rs11153177	0.95[EUR][1000 genomes]
rs11153180	0.95[EUR][1000 genomes]
rs11153181	0.95[EUR][1000 genomes]
rs11753645	0.80[CEU][hapmap]
rs11967108	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs12190920	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12190996	0.86[EUR][1000 genomes]
rs12192847	0.87[EUR][1000 genomes]
rs12193493	0.92[EUR][1000 genomes]
rs12197114	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs12206928	0.89[EUR][1000 genomes]
rs12208933	0.90[CEU][hapmap]
rs12209691	0.87[EUR][1000 genomes]
rs12213313	0.95[EUR][1000 genomes]
rs12524273	0.93[EUR][1000 genomes]
rs12524639	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs12528712	0.81[CEU][hapmap]
rs12528822	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs13195517	0.81[CEU][hapmap]
rs13199519	0.85[CEU][hapmap]
rs13212766	0.91[EUR][1000 genomes]
rs1322816	0.92[EUR][1000 genomes]
rs1358997	0.93[EUR][1000 genomes]
rs1358998	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1546980	0.89[EUR][1000 genomes]
rs1590306	0.92[EUR][1000 genomes]
rs17070591	0.86[YRI][hapmap]
rs1923725	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2236582	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs2275650	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs34202013	0.91[EUR][1000 genomes]
rs35056702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035949	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36099706	0.95[EUR][1000 genomes]
rs3757234	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs3757235	0.83[MKK][hapmap]
rs3778475	0.92[EUR][1000 genomes]
rs3778477	0.88[EUR][1000 genomes]
rs3799835	0.81[CEU][hapmap]
rs3799839	0.93[EUR][1000 genomes]
rs3807005	0.87[EUR][1000 genomes]
rs3818934	0.91[EUR][1000 genomes]
rs59056467	0.83[EUR][1000 genomes]
rs59906308	0.94[EUR][1000 genomes]
rs68042406	0.83[EUR][1000 genomes]
rs6911838	0.90[CEU][hapmap]
rs6914498	0.90[CEU][hapmap]
rs6920962	0.91[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6929023	0.93[EUR][1000 genomes]
rs730089	0.82[MKK][hapmap]
rs736830	0.84[MKK][hapmap]
rs7372	0.92[EUR][1000 genomes]
rs752262	0.89[EUR][1000 genomes]
rs7773095	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9320287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480933	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480948	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9480951	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9480953	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480957	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs9487068	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487097	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9487098	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487100	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs9487103	0.84[MKK][hapmap]
rs974034	0.83[MKK][hapmap]
rs9885646	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[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17070580	MICAL1	cis	parietal	SCAN
rs17070580	SMPD2	cis	multi-tissue	Pritchard
rs17070580	PPIL6	cis	brain	seeQTL
rs17070580	PDSS2	cis	cerebellum	SCAN
rs17070580	AKD1	cis	cerebellum	SCAN
rs17070580	SMPD2	cis	cerebellum	SCAN
rs17070580	SMPD2	cis	parietal	SCAN
rs17070580	SMPD2	cis	Whole Blood	GTEx
rs17070580	CD164	cis	parietal	SCAN
rs17070580	ZBTB24	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
2	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
4	chr6:109724400-109750400	Weak transcription	Ovary	ovary
5	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
6	chr6:109731400-109745200	Weak transcription	Pancreas	Pancrea
7	chr6:109735200-109750200	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:109735600-109750000	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:109735800-109742000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:109736400-109740400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:109736600-109760800	Weak transcription	Brain Angular Gyrus	brain
12	chr6:109737000-109745400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:109737000-109745400	Weak transcription	Left Ventricle	heart
14	chr6:109737400-109750200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:109738400-109739200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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