Variant report

Variant	rs62465367
Chromosome Location	chr7:65849657-65849658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65578865..65581340-chr7:65848179..65850812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 170 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs12530506	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12530546	0.95[EUR][1000 genomes]
rs12530746	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530947	0.97[EUR][1000 genomes]
rs12531900	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532060	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532173	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532182	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532247	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532249	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532278	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532383	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532423	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12532657	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532675	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12533387	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12533744	0.87[EUR][1000 genomes]
rs12533877	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12534039	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12534109	0.87[EUR][1000 genomes]
rs12534249	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12534263	0.95[EUR][1000 genomes]
rs12534477	0.87[EUR][1000 genomes]
rs12534881	0.83[EUR][1000 genomes]
rs12534985	0.97[EUR][1000 genomes]
rs12535985	0.87[EUR][1000 genomes]
rs12536816	0.87[EUR][1000 genomes]
rs12536818	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12537037	0.97[EUR][1000 genomes]
rs12537039	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537368	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537698	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537936	0.87[EUR][1000 genomes]
rs12538011	0.95[EUR][1000 genomes]
rs12538113	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538147	0.87[EUR][1000 genomes]
rs12538379	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12538611	0.86[ASN][1000 genomes]
rs12538686	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12538961	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12539116	0.97[EUR][1000 genomes]
rs12539696	0.92[EUR][1000 genomes]
rs12539749	0.97[EUR][1000 genomes]
rs12539795	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12540455	0.97[EUR][1000 genomes]
rs12540667	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12540888	0.87[EUR][1000 genomes]
rs1363056	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17228285	0.95[EUR][1000 genomes]
rs17294397	0.97[EUR][1000 genomes]
rs2075004	0.97[EUR][1000 genomes]
rs2292936	0.87[EUR][1000 genomes]
rs2292937	0.87[EUR][1000 genomes]
rs35910256	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735145	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3735146	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735150	0.97[EUR][1000 genomes]
rs3814466	0.97[EUR][1000 genomes]
rs3815684	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149467	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717291	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4717301	0.97[EUR][1000 genomes]
rs4717305	0.97[EUR][1000 genomes]
rs4718342	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718345	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718347	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718350	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718353	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718354	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718368	0.97[EUR][1000 genomes]
rs4718372	0.95[EUR][1000 genomes]
rs4718376	0.97[EUR][1000 genomes]
rs4718379	0.97[EUR][1000 genomes]
rs4718380	0.97[EUR][1000 genomes]
rs62465362	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465363	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465365	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465372	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465373	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465376	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465377	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465380	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465389	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465390	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465391	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465392	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465394	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465395	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465396	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465397	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465399	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465400	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465401	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62465402	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465403	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465404	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465405	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465422	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465424	0.97[EUR][1000 genomes]
rs62465425	0.97[EUR][1000 genomes]
rs62465426	0.95[EUR][1000 genomes]
rs62465428	0.97[EUR][1000 genomes]
rs62465429	0.97[EUR][1000 genomes]
rs62465431	0.97[EUR][1000 genomes]
rs62465432	0.95[EUR][1000 genomes]
rs62465433	0.92[EUR][1000 genomes]
rs62465436	0.82[EUR][1000 genomes]
rs62465457	0.97[EUR][1000 genomes]
rs62465458	0.97[EUR][1000 genomes]
rs62465474	0.82[EUR][1000 genomes]
rs62465475	0.82[EUR][1000 genomes]
rs62465476	0.84[EUR][1000 genomes]
rs62465483	0.80[EUR][1000 genomes]
rs62465484	0.87[EUR][1000 genomes]
rs62465512	0.87[EUR][1000 genomes]
rs62465513	0.87[EUR][1000 genomes]
rs62465515	0.87[EUR][1000 genomes]
rs62465519	0.87[EUR][1000 genomes]
rs62465521	0.87[EUR][1000 genomes]
rs62465522	0.87[EUR][1000 genomes]
rs62465525	0.87[EUR][1000 genomes]
rs62465526	0.87[EUR][1000 genomes]
rs62465527	0.87[EUR][1000 genomes]
rs62465542	0.87[EUR][1000 genomes]
rs62465545	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62465546	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62465547	0.87[AMR][1000 genomes]
rs62465550	0.87[AMR][1000 genomes]
rs62465552	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465554	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62467760	0.95[EUR][1000 genomes]
rs62467762	0.97[EUR][1000 genomes]
rs62467763	0.97[EUR][1000 genomes]
rs62467764	0.97[EUR][1000 genomes]
rs62467765	0.97[EUR][1000 genomes]
rs62467766	0.97[EUR][1000 genomes]
rs62467767	0.90[EUR][1000 genomes]
rs62467768	0.92[EUR][1000 genomes]
rs62467769	0.97[EUR][1000 genomes]
rs62467770	0.97[EUR][1000 genomes]
rs62467771	0.95[EUR][1000 genomes]
rs62467801	0.95[EUR][1000 genomes]
rs62467802	0.97[EUR][1000 genomes]
rs62467804	0.97[EUR][1000 genomes]
rs62467805	0.97[EUR][1000 genomes]
rs62467811	0.97[EUR][1000 genomes]
rs62468669	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62468673	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62468674	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468677	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468679	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468696	0.97[EUR][1000 genomes]
rs62468699	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468700	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62468702	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468705	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468707	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468708	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468709	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62468710	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62468711	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468712	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv970513	chr7:65842694-65860742	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv981506	chr7:65842694-65876873	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465367	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65840000-65878400	Weak transcription	Psoas Muscle	Psoas
2	chr7:65840400-65873400	Weak transcription	K562	blood
3	chr7:65840600-65858400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:65841400-65875400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:65842400-65867800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:65843400-65877600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:65843600-65878200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:65843800-65851000	Weak transcription	GM12878-XiMat	blood
9	chr7:65844000-65878400	Weak transcription	Thymus	Thymus
10	chr7:65844600-65860400	Weak transcription	Esophagus	oesophagus
11	chr7:65845000-65856000	Weak transcription	Right Atrium	heart
12	chr7:65845000-65866800	Weak transcription	Brain Anterior Caudate	brain
13	chr7:65845000-65867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:65845000-65867200	Weak transcription	Spleen	Spleen
15	chr7:65845000-65873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:65845000-65873600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:65845000-65878000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:65845000-65878000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:65845000-65878200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:65845000-65878200	Weak transcription	Right Ventricle	heart
21	chr7:65845000-65878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:65845000-65878400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr7:65845000-65878400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:65845200-65850000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:65845200-65850400	Weak transcription	Lung	lung
26	chr7:65845200-65856200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:65845200-65867200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr7:65845200-65873400	Weak transcription	HepG2	liver
29	chr7:65845200-65878200	Weak transcription	Left Ventricle	heart
30	chr7:65845200-65878600	Weak transcription	Aorta	Aorta
31	chr7:65845400-65853600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:65845400-65854200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:65845400-65856400	Weak transcription	Fetal Intestine Large	intestine
34	chr7:65845400-65860400	Weak transcription	Osteobl	bone
35	chr7:65845400-65863400	Weak transcription	Brain Angular Gyrus	brain
36	chr7:65845400-65864200	Weak transcription	Primary T cells from cord blood	blood
37	chr7:65845400-65865600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:65845400-65866600	Weak transcription	Adipose Nuclei	Adipose
39	chr7:65845400-65875400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:65845400-65877200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:65845400-65878000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:65845400-65878200	Weak transcription	Brain Germinal Matrix	brain
43	chr7:65845400-65878200	Weak transcription	Pancreas	Pancrea
44	chr7:65845600-65849800	Weak transcription	NHEK	skin
45	chr7:65845600-65850000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:65845600-65855800	Weak transcription	Fetal Intestine Small	intestine
47	chr7:65845600-65857200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:65845600-65860400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:65845600-65864000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:65845600-65864000	Weak transcription	Brain Substantia Nigra	brain

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