Variant report

Variant	rs11130138
Chromosome Location	chr3:47598663-47598664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47597172..47600362-chr3:47601901..47605676,3	K562	blood:
2	chr3:47597484..47600327-chr3:47607469..47609987,3	K562	blood:
3	chr3:47597539..47601174-chr3:47612782..47615895,3	K562	blood:

Variant related genes	Relation type
ENSG00000244732	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1014228	0.94[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs10865948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130139	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11130143	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130144	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130145	0.82[AMR][1000 genomes]
rs11130146	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs11130147	0.81[AMR][1000 genomes]
rs11130148	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs11712464	0.88[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap]
rs11714942	0.82[AMR][1000 genomes]
rs11716582	0.88[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11929303	0.86[EUR][1000 genomes]
rs12489865	0.88[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs12492915	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12495204	0.83[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs12497921	0.83[AMR][1000 genomes]
rs12498027	0.85[AMR][1000 genomes]
rs12635438	0.88[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap]
rs12636198	0.90[EUR][1000 genomes]
rs12636863	0.85[AMR][1000 genomes]
rs13061412	0.86[CEU][hapmap];0.82[AMR][1000 genomes]
rs13063042	0.87[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs13064183	0.82[AMR][1000 genomes]
rs13081356	0.82[AMR][1000 genomes]
rs13084555	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13085978	0.87[EUR][1000 genomes]
rs13086149	0.84[AMR][1000 genomes]
rs13091913	0.81[AMR][1000 genomes]
rs13094264	0.88[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs13098128	0.83[AMR][1000 genomes]
rs1403578	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1403579	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1464614	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1486915	0.83[AMR][1000 genomes]
rs17079785	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs2030596	0.83[AMR][1000 genomes]
rs2047559	0.88[CEU][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs2133601	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.80[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs2140335	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs2280567	0.88[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2291903	0.86[JPT][hapmap]
rs2293226	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2882611	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs34252990	0.80[EUR][1000 genomes]
rs34351471	0.82[AMR][1000 genomes]
rs34616865	0.84[EUR][1000 genomes]
rs35148469	0.82[AMR][1000 genomes]
rs35167544	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35533636	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35698005	0.83[AMR][1000 genomes]
rs3732530	0.94[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3755637	0.84[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755638	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3772403	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4274776	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4858801	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4858835	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858842	0.88[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858846	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs4858851	0.88[CEU][hapmap];0.89[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs4858857	0.81[AMR][1000 genomes]
rs56746603	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60110914	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60322343	0.90[EUR][1000 genomes]
rs60992717	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61181421	0.81[AMR][1000 genomes]
rs61620099	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61675361	0.87[EUR][1000 genomes]
rs6442070	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442071	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442072	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6442074	0.81[AMR][1000 genomes]
rs6442082	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs6442083	0.82[AMR][1000 genomes]
rs6442085	0.81[AMR][1000 genomes]
rs6767896	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6767996	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6768699	0.83[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs6772301	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs6774170	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6777632	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs6780080	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6780395	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6782707	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6784946	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785669	0.88[CEU][hapmap];0.89[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs6786001	0.83[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs6789835	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792350	0.82[AMR][1000 genomes]
rs6792497	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[YRI][hapmap]
rs6792737	0.82[AMR][1000 genomes]
rs6806860	0.94[CHB][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs7429162	0.84[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs7612219	0.82[AMR][1000 genomes]
rs7613934	0.88[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7618758	0.83[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs7621236	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7624474	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7631950	0.94[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7637372	0.83[AMR][1000 genomes]
rs7638103	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs7642691	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7645846	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs868255	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs869508	0.88[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs870622	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs883661	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs883662	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs883663	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9311409	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9681917	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs9757517	0.81[AMR][1000 genomes]
rs9820051	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9835605	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11130138	SMARCC1	cis	parietal	SCAN
rs11130138	ZNF589	cis	parietal	SCAN
rs11130138	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs11130138	ZNF589	cis	Nerve Tibial	GTEx
rs11130138	ZNF589	cis	cerebellum	SCAN
rs11130138	HYAL2	cis	cerebellum	SCAN
rs11130138	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs11130138	MRPS18AP1	cis	Nerve Tibial	GTEx
rs11130138	MRPS18AP1	cis	lung	GTEx
rs11130138	SMARCC1	cis	cerebellum	SCAN

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	chr3:47595200-47602800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:47595200-47605400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:47595200-47605600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:47595200-47612600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:47595400-47606600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:47596800-47607400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:47596800-47612400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:47598000-47599000	Enhancers	Colon Smooth Muscle	Colon
10	chr3:47598000-47599000	Enhancers	Fetal Heart	heart
11	chr3:47598000-47599000	Enhancers	K562	blood
12	chr3:47598200-47598800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:47598200-47599000	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:47598400-47599600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:47598400-47600000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:47598400-47602800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:47598600-47606000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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