Variant report

Variant	rs12489865
Chromosome Location	chr3:47608337-47608338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47597484..47600327-chr3:47607469..47609987,3	K562	blood:
2	chr3:47607614..47610725-chr3:47619552..47621831,5	K562	blood:
3	chr3:47606452..47609238-chr3:47614445..47617040,2	K562	blood:

Variant related genes	Relation type
ENSG00000114646	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1014228	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865948	0.88[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs11130138	0.88[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs11130139	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130143	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs11130144	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs11130146	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs11130148	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs11712464	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs11716582	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs11929303	0.81[EUR][1000 genomes]
rs12495204	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs12635438	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs12636198	0.86[EUR][1000 genomes]
rs13061412	1.00[CEU][hapmap]
rs13063042	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap]
rs13085978	0.83[EUR][1000 genomes]
rs13091913	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs13094264	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs1403578	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs1403579	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs1464614	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs17079785	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs2047559	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs2049300	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2133601	0.88[ASW][hapmap];0.92[CEU][hapmap];0.82[GIH][hapmap];0.93[YRI][hapmap]
rs2140335	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs2280567	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293226	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2882611	1.00[CEU][hapmap]
rs34616865	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35167544	0.80[EUR][1000 genomes]
rs36033865	0.87[AMR][1000 genomes]
rs3732530	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755637	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs3755638	0.86[EUR][1000 genomes]
rs3772403	0.86[EUR][1000 genomes]
rs4274776	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs4858801	0.92[CEU][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs4858842	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs4858846	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs4858851	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs60110914	0.85[EUR][1000 genomes]
rs60322343	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61620099	0.83[EUR][1000 genomes]
rs61675361	0.83[EUR][1000 genomes]
rs6442082	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs6768699	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs6772301	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs6774170	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs6777632	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6785669	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs6786001	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs6792497	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6806860	0.89[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap]
rs7429162	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs7613934	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs7618758	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap]
rs7621236	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs7624474	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs7631950	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs7638103	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs7645846	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs868255	0.81[EUR][1000 genomes]
rs869508	1.00[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs870622	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs883661	0.80[EUR][1000 genomes]
rs883662	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs883663	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs9681917	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12489865	SMARCC1	cis	cerebellum	SCAN
rs12489865	ZNF589	cis	Nerve Tibial	GTEx
rs12489865	FCF1P2	cis	Artery Tibial	GTEx
rs12489865	ZNF589	cis	cerebellum	SCAN
rs12489865	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs12489865	MRPS18AP1	cis	lung	GTEx
rs12489865	HYAL2	cis	cerebellum	SCAN
rs12489865	MRPS18AP1	cis	Nerve Tibial	GTEx
rs12489865	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs12489865	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs12489865	ZNF589	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47595200-47612600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:47596800-47612400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47599000-47609400	Weak transcription	K562	blood
4	chr3:47602800-47611800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:47602800-47612400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:47603000-47610800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:47604400-47610800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47604600-47611000	Strong transcription	Fetal Brain Female	brain
9	chr3:47605000-47612800	Weak transcription	Fetal Brain Male	brain
10	chr3:47605400-47610800	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr3:47606000-47608800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:47606600-47612600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:47607200-47612600	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:47607600-47612600	Weak transcription	Brain Angular Gyrus	brain
15	chr3:47607800-47609000	Strong transcription	Brain Germinal Matrix	brain
16	chr3:47608000-47608800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:47608200-47608600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:47608200-47610800	Strong transcription	Brain Anterior Caudate	brain

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