Variant report

Variant	rs12537825
Chromosome Location	chr7:66381151-66381152
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66379712..66381222-chr7:66384887..66387330,2	K562	blood:
2	chr7:66377019..66378692-chr7:66380381..66382203,2	K562	blood:
3	chr7:66380078..66382132-chr7:66461899..66464169,2	MCF-7	breast:
4	chr7:66379191..66382749-chr7:66384574..66388642,5	K562	blood:
5	chr7:66378566..66381625-chr7:66385153..66387745,3	MCF-7	breast:
6	chr7:66380772..66383559-chr7:66384336..66386339,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10499785	0.82[ASN][1000 genomes]
rs12531377	0.82[ASN][1000 genomes]
rs12531516	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532160	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12532307	0.87[AMR][1000 genomes]
rs12532650	0.87[AMR][1000 genomes]
rs12532888	0.82[ASN][1000 genomes]
rs12533830	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12533958	0.82[ASN][1000 genomes]
rs12534278	0.81[AMR][1000 genomes]
rs12534401	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12535023	0.81[AMR][1000 genomes]
rs12535268	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12536130	0.82[ASN][1000 genomes]
rs12537353	0.81[AMR][1000 genomes]
rs12537403	0.80[EUR][1000 genomes]
rs12537414	0.81[AMR][1000 genomes]
rs12537771	0.80[EUR][1000 genomes]
rs12537955	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12538126	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12539191	0.80[EUR][1000 genomes]
rs12539366	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12539522	0.80[EUR][1000 genomes]
rs12539848	0.82[ASN][1000 genomes]
rs12540312	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12540447	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12540536	0.80[EUR][1000 genomes]
rs12540695	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17567255	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2091314	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293351	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34758320	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35279320	0.82[ASN][1000 genomes]
rs35448884	0.81[AMR][1000 genomes]
rs3735153	0.82[ASN][1000 genomes]
rs3778911	0.82[ASN][1000 genomes]
rs3800819	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4717311	0.80[EUR][1000 genomes]
rs4717312	0.80[EUR][1000 genomes]
rs4717313	0.80[EUR][1000 genomes]
rs4717314	0.80[EUR][1000 genomes]
rs4717316	0.80[EUR][1000 genomes]
rs4717323	0.87[AMR][1000 genomes]
rs4717324	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4717329	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4717332	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718390	0.80[EUR][1000 genomes]
rs4718391	0.80[EUR][1000 genomes]
rs4718392	0.80[EUR][1000 genomes]
rs4718407	0.82[ASN][1000 genomes]
rs4718409	0.82[ASN][1000 genomes]
rs4718426	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718434	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4718450	0.81[AMR][1000 genomes]
rs62464646	0.82[ASN][1000 genomes]
rs62464647	0.82[ASN][1000 genomes]
rs62464648	0.82[ASN][1000 genomes]
rs62464651	0.82[ASN][1000 genomes]
rs62464652	0.82[ASN][1000 genomes]
rs62464653	0.82[ASN][1000 genomes]
rs62464654	0.82[ASN][1000 genomes]
rs62464655	0.82[ASN][1000 genomes]
rs62464658	0.82[ASN][1000 genomes]
rs62464659	0.82[ASN][1000 genomes]
rs62465676	0.82[ASN][1000 genomes]
rs62465678	0.82[ASN][1000 genomes]
rs62465681	0.82[ASN][1000 genomes]
rs62465682	0.82[ASN][1000 genomes]
rs62465688	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62465698	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62465699	0.81[AMR][1000 genomes]
rs62465700	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62465701	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62465705	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62465706	0.81[AMR][1000 genomes]
rs62465707	0.81[AMR][1000 genomes]
rs62465709	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62465710	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465712	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465713	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465714	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465716	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465730	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465734	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62465736	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465738	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465739	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465740	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465741	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465742	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465743	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465744	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465745	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465747	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465748	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465750	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465752	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62466127	0.80[EUR][1000 genomes]
rs62466128	0.80[EUR][1000 genomes]
rs62466133	0.80[EUR][1000 genomes]
rs62466134	0.80[EUR][1000 genomes]
rs62466136	0.80[EUR][1000 genomes]
rs62466137	0.80[EUR][1000 genomes]
rs62466138	0.80[EUR][1000 genomes]
rs62466139	0.80[EUR][1000 genomes]
rs62466144	0.80[EUR][1000 genomes]
rs62466145	0.80[EUR][1000 genomes]
rs62466146	0.80[EUR][1000 genomes]
rs62466147	0.80[EUR][1000 genomes]
rs62466148	0.80[EUR][1000 genomes]
rs62466575	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466578	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466582	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466584	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466586	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466588	0.93[AMR][1000 genomes]
rs62466589	0.93[AMR][1000 genomes]
rs62466632	0.81[AMR][1000 genomes]
rs62466633	0.81[AMR][1000 genomes]
rs62466634	0.81[AMR][1000 genomes]
rs62466635	0.81[AMR][1000 genomes]
rs62466637	0.81[AMR][1000 genomes]
rs62466638	0.81[AMR][1000 genomes]
rs62466639	0.81[AMR][1000 genomes]
rs62466640	0.81[AMR][1000 genomes]
rs62466642	0.81[AMR][1000 genomes]
rs62466657	0.81[AMR][1000 genomes]
rs62466659	0.81[AMR][1000 genomes]
rs62466787	0.80[EUR][1000 genomes]
rs62466788	0.80[EUR][1000 genomes]
rs62466789	0.80[EUR][1000 genomes]
rs62466792	0.80[EUR][1000 genomes]
rs62466795	0.80[EUR][1000 genomes]
rs62466797	0.80[EUR][1000 genomes]
rs62466798	0.80[EUR][1000 genomes]
rs62466801	0.80[EUR][1000 genomes]
rs62466802	0.80[EUR][1000 genomes]
rs62468261	0.82[ASN][1000 genomes]
rs62468262	0.82[ASN][1000 genomes]
rs62468263	0.82[ASN][1000 genomes]
rs62468374	0.81[AMR][1000 genomes]
rs62468375	0.81[AMR][1000 genomes]
rs62468378	0.81[AMR][1000 genomes]
rs62468379	0.81[AMR][1000 genomes]
rs62468380	0.81[AMR][1000 genomes]
rs62468381	0.81[AMR][1000 genomes]
rs62468382	0.81[AMR][1000 genomes]
rs7781008	0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12537825	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
3	chr7:66350600-66385200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:66364400-66385400	Weak transcription	HSMMtube	muscle
5	chr7:66364800-66385000	Weak transcription	Brain Anterior Caudate	brain
6	chr7:66366400-66385600	Weak transcription	Brain Substantia Nigra	brain
7	chr7:66368000-66385400	Weak transcription	Adipose Nuclei	Adipose
8	chr7:66369000-66385400	Weak transcription	Thymus	Thymus
9	chr7:66369000-66385600	Weak transcription	Ovary	ovary
10	chr7:66370000-66385200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:66370200-66385400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:66370800-66385000	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:66371000-66385200	Weak transcription	Fetal Muscle Leg	muscle
14	chr7:66371200-66382000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:66371200-66385400	Weak transcription	Fetal Intestine Small	intestine
16	chr7:66371200-66385600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:66371800-66382400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:66371800-66385400	Weak transcription	Fetal Stomach	stomach
19	chr7:66373000-66382600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:66377400-66381800	Weak transcription	Liver	Liver
21	chr7:66379000-66385200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:66379400-66384200	Weak transcription	K562	blood
23	chr7:66380600-66381200	Enhancers	HepG2	liver
24	chr7:66380800-66384800	Weak transcription	GM12878-XiMat	blood

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