Variant report

Variant	rs62465380
Chromosome Location	chr7:65898575-65898576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs12530506	0.97[EUR][1000 genomes]
rs12530546	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12530746	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12530947	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12531758	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12531900	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12532060	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532173	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532182	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532247	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532249	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532267	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12532278	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532383	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532423	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12532657	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532675	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12533387	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12533744	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12533877	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533963	0.95[EUR][1000 genomes]
rs12534039	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12534249	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12534263	0.97[EUR][1000 genomes]
rs12534477	0.89[EUR][1000 genomes]
rs12534881	0.85[EUR][1000 genomes]
rs12534985	1.00[EUR][1000 genomes]
rs12535756	1.00[EUR][1000 genomes]
rs12536586	1.00[EUR][1000 genomes]
rs12536816	0.89[EUR][1000 genomes]
rs12536818	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537037	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12537039	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12537368	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537698	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12538011	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12538113	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12538147	0.89[EUR][1000 genomes]
rs12538379	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12538611	1.00[ASN][1000 genomes]
rs12538686	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12538961	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12539116	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12539696	0.95[EUR][1000 genomes]
rs12539749	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12539795	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12540455	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12540667	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12540888	0.89[EUR][1000 genomes]
rs1363056	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17228285	0.97[EUR][1000 genomes]
rs17228728	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17229513	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17229674	1.00[EUR][1000 genomes]
rs17294397	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2075004	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35910256	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735145	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735146	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735150	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3814466	1.00[EUR][1000 genomes]
rs3815684	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4149467	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4717291	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4717301	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4717305	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4718342	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718345	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718347	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718350	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718353	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718354	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718368	1.00[EUR][1000 genomes]
rs4718372	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4718376	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4718379	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4718380	1.00[EUR][1000 genomes]
rs4718381	0.95[EUR][1000 genomes]
rs4718382	1.00[EUR][1000 genomes]
rs62465362	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465363	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465364	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465365	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465367	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465372	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465373	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62465376	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465377	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465389	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465390	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465391	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465392	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465394	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465395	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465396	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465397	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465399	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62465400	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465401	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62465402	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465403	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465404	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465405	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465422	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465424	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465425	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62465426	0.97[EUR][1000 genomes]
rs62465427	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62465428	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465429	1.00[EUR][1000 genomes]
rs62465431	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465432	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62465433	0.95[EUR][1000 genomes]
rs62465436	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62465457	1.00[EUR][1000 genomes]
rs62465458	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62465519	0.89[EUR][1000 genomes]
rs62465521	0.89[EUR][1000 genomes]
rs62465522	0.89[EUR][1000 genomes]
rs62465525	0.89[EUR][1000 genomes]
rs62465526	0.89[EUR][1000 genomes]
rs62465527	0.89[EUR][1000 genomes]
rs62465542	0.89[EUR][1000 genomes]
rs62465545	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62465546	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465547	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465550	0.87[AMR][1000 genomes]
rs62465552	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465554	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62466081	1.00[EUR][1000 genomes]
rs62467760	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62467762	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467763	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467764	1.00[EUR][1000 genomes]
rs62467765	1.00[EUR][1000 genomes]
rs62467766	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467767	0.92[EUR][1000 genomes]
rs62467768	0.95[EUR][1000 genomes]
rs62467769	1.00[EUR][1000 genomes]
rs62467770	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467771	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62467801	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62467802	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467804	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467805	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467811	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467814	1.00[EUR][1000 genomes]
rs62467816	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62467856	0.97[EUR][1000 genomes]
rs62468669	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62468673	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62468674	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62468677	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62468679	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62468696	1.00[EUR][1000 genomes]
rs62468699	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62468700	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62468702	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468705	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468707	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62468708	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62468709	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62468710	0.88[ASN][1000 genomes]
rs62468711	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62468712	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62469060	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62469061	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62469062	1.00[EUR][1000 genomes]
rs62469064	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62469066	1.00[EUR][1000 genomes]
rs62469067	1.00[EUR][1000 genomes]
rs62469069	1.00[EUR][1000 genomes]
rs62469070	1.00[EUR][1000 genomes]
rs62469072	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7384751	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv970867	chr7:65893874-65900243	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465380	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879000-65905600	Weak transcription	Lung	lung
2	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
4	chr7:65879200-65902000	Weak transcription	Brain Substantia Nigra	brain
5	chr7:65879200-65904000	Weak transcription	Fetal Lung	lung
6	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
7	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
8	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:65879200-65946000	Weak transcription	NHEK	skin
10	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
11	chr7:65879400-65900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:65879400-65901000	Weak transcription	Brain Angular Gyrus	brain
13	chr7:65879400-65901200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
16	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
17	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
20	chr7:65879600-65899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:65879600-65900600	Weak transcription	Brain Germinal Matrix	brain
22	chr7:65879600-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:65879600-65920400	Weak transcription	Primary B cells from cord blood	blood
26	chr7:65879800-65913600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:65884000-65919600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:65885000-65904200	Weak transcription	K562	blood
29	chr7:65886000-65913600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:65886600-65920400	Weak transcription	Right Ventricle	heart
31	chr7:65887000-65924600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:65887000-65924600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:65887200-65904600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:65889200-65903000	Weak transcription	Thymus	Thymus
35	chr7:65889200-65939600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr7:65889600-65913800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:65890000-65928800	Weak transcription	Adipose Nuclei	Adipose
38	chr7:65890200-65907400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:65890400-65916200	Weak transcription	Fetal Thymus	thymus
40	chr7:65891400-65902000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:65891600-65939000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:65892000-65931800	Weak transcription	Ovary	ovary
43	chr7:65893200-65913400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:65894200-65899800	Weak transcription	Spleen	Spleen
45	chr7:65894200-65905400	Weak transcription	Gastric	stomach
46	chr7:65894200-65939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:65894600-65899400	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:65894600-65905200	Weak transcription	Pancreas	Pancrea
49	chr7:65894800-65914000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr7:65895000-65899400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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