Variant report

Variant	rs11716779
Chromosome Location	chr3:47606215-47606216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11709289	0.86[AMR][1000 genomes]
rs11711725	0.88[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs17785248	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34448818	0.82[AMR][1000 genomes]
rs35012836	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5016900	0.82[AMR][1000 genomes]
rs62262084	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs11716779	SMARCC1	Cis_1M	lymphoblastoid	RTeQTL
rs11716779	HYAL2	cis	cerebellum	SCAN
rs11716779	CDC25A	cis	Muscle Skeletal	GTEx
rs11716779	NME6	cis	Esophagus Muscularis	GTEx
rs11716779	ZNF589	cis	parietal	SCAN
rs11716779	MRPS18AP1	cis	Nerve Tibial	GTEx
rs11716779	MRPS18AP1	cis	Artery Tibial	GTEx
rs11716779	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs11716779	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs11716779	ZNF589	cis	cerebellum	SCAN
rs11716779	SMARCC1	cis	cerebellum	SCAN
rs11716779	MRPS18AP1	cis	Thyroid	GTEx
rs11716779	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs11716779	ZNF589	cis	Nerve Tibial	GTEx
rs11716779	ZNF589	cis	Esophagus Muscularis	GTEx
rs11716779	CDC25A	cis	Thyroid	GTEx
rs11716779	MRPS18AP1	cis	lung	GTEx
rs11716779	GNAI2	cis	parietal	SCAN
rs11716779	ZNF589	cis	Artery Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47584200-47607800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:47595200-47612600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:47595400-47606600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:47596800-47607400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:47596800-47612400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47599000-47609400	Weak transcription	K562	blood
7	chr3:47602800-47611800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:47602800-47612400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:47603000-47610800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:47604200-47607600	Strong transcription	Brain Angular Gyrus	brain
11	chr3:47604400-47610800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47604600-47611000	Strong transcription	Fetal Brain Female	brain
13	chr3:47605000-47612800	Weak transcription	Fetal Brain Male	brain
14	chr3:47605400-47610800	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr3:47605600-47606600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr3:47606000-47608800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:47606200-47607400	Strong transcription	Brain Anterior Caudate	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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