Variant report

Variant	rs62465741
Chromosome Location	chr7:66365968-66365969
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	chr7:66365153..66367463-chr7:66373065..66375553,2	MCF-7	breast:

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10499785	0.85[ASN][1000 genomes]
rs12531377	0.85[ASN][1000 genomes]
rs12531516	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12531690	0.82[EUR][1000 genomes]
rs12532160	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12532888	0.85[ASN][1000 genomes]
rs12533830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12533886	0.80[EUR][1000 genomes]
rs12533958	0.85[ASN][1000 genomes]
rs12534401	0.85[ASN][1000 genomes]
rs12535268	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12536130	0.85[ASN][1000 genomes]
rs12537403	0.84[EUR][1000 genomes]
rs12537771	0.84[EUR][1000 genomes]
rs12537825	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538126	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12539191	0.84[EUR][1000 genomes]
rs12539366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539522	0.84[EUR][1000 genomes]
rs12539848	0.85[ASN][1000 genomes]
rs12540312	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540536	0.84[EUR][1000 genomes]
rs12540695	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17567255	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34758320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35279320	0.85[ASN][1000 genomes]
rs3735153	0.85[ASN][1000 genomes]
rs3778911	0.85[ASN][1000 genomes]
rs3800819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717309	0.84[EUR][1000 genomes]
rs4717311	0.84[EUR][1000 genomes]
rs4717312	0.84[EUR][1000 genomes]
rs4717313	0.84[EUR][1000 genomes]
rs4717314	0.84[EUR][1000 genomes]
rs4717316	0.84[EUR][1000 genomes]
rs4717323	0.81[AMR][1000 genomes]
rs4717324	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4717329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718390	0.84[EUR][1000 genomes]
rs4718391	0.84[EUR][1000 genomes]
rs4718392	0.84[EUR][1000 genomes]
rs4718407	0.85[ASN][1000 genomes]
rs4718409	0.85[ASN][1000 genomes]
rs4718426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718434	0.82[ASN][1000 genomes]
rs62464646	0.85[ASN][1000 genomes]
rs62464647	0.85[ASN][1000 genomes]
rs62464648	0.85[ASN][1000 genomes]
rs62464651	0.85[ASN][1000 genomes]
rs62464652	0.85[ASN][1000 genomes]
rs62464653	0.85[ASN][1000 genomes]
rs62464654	0.85[ASN][1000 genomes]
rs62464655	0.85[ASN][1000 genomes]
rs62464658	0.85[ASN][1000 genomes]
rs62464659	0.85[ASN][1000 genomes]
rs62465676	0.85[ASN][1000 genomes]
rs62465678	0.85[ASN][1000 genomes]
rs62465681	0.85[ASN][1000 genomes]
rs62465682	0.85[ASN][1000 genomes]
rs62465688	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465698	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465699	0.87[AMR][1000 genomes]
rs62465700	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465701	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465705	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465706	0.87[AMR][1000 genomes]
rs62465707	0.87[AMR][1000 genomes]
rs62465709	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465710	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465712	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465713	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465714	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465716	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465730	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466123	0.84[EUR][1000 genomes]
rs62466126	0.84[EUR][1000 genomes]
rs62466127	0.84[EUR][1000 genomes]
rs62466128	0.84[EUR][1000 genomes]
rs62466133	0.84[EUR][1000 genomes]
rs62466134	0.84[EUR][1000 genomes]
rs62466136	0.84[EUR][1000 genomes]
rs62466137	0.84[EUR][1000 genomes]
rs62466138	0.84[EUR][1000 genomes]
rs62466139	0.84[EUR][1000 genomes]
rs62466142	0.82[EUR][1000 genomes]
rs62466143	0.82[EUR][1000 genomes]
rs62466144	0.84[EUR][1000 genomes]
rs62466145	0.84[EUR][1000 genomes]
rs62466146	0.84[EUR][1000 genomes]
rs62466147	0.84[EUR][1000 genomes]
rs62466148	0.84[EUR][1000 genomes]
rs62466575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466578	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466582	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466584	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466586	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62466588	0.87[AMR][1000 genomes]
rs62466589	0.87[AMR][1000 genomes]
rs62466787	0.84[EUR][1000 genomes]
rs62466788	0.84[EUR][1000 genomes]
rs62466789	0.84[EUR][1000 genomes]
rs62466792	0.84[EUR][1000 genomes]
rs62466795	0.84[EUR][1000 genomes]
rs62466797	0.84[EUR][1000 genomes]
rs62466798	0.84[EUR][1000 genomes]
rs62466799	0.80[EUR][1000 genomes]
rs62466801	0.84[EUR][1000 genomes]
rs62466802	0.84[EUR][1000 genomes]
rs62468261	0.85[ASN][1000 genomes]
rs62468262	0.85[ASN][1000 genomes]
rs62468263	0.85[ASN][1000 genomes]
rs7781008	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv981514	chr7:66310139-66366240	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465741	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
2	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
4	chr7:66321200-66367800	Weak transcription	Aorta	Aorta
5	chr7:66325200-66366400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:66325400-66366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:66325400-66369400	Weak transcription	Fetal Brain Female	brain
8	chr7:66325600-66373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:66325800-66366400	Weak transcription	Right Ventricle	heart
10	chr7:66325800-66367000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:66325800-66367600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:66326400-66368200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:66326400-66371800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:66328200-66367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:66329800-66372000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr7:66330400-66366000	Weak transcription	Fetal Thymus	thymus
17	chr7:66331800-66378400	Weak transcription	A549	lung
18	chr7:66333000-66371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:66333800-66371800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:66334200-66367600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:66335400-66371400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr7:66336200-66366400	Weak transcription	Thymus	Thymus
23	chr7:66336200-66369400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr7:66342800-66370600	Weak transcription	NHLF	lung
25	chr7:66343000-66367600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:66344600-66368200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:66345600-66368400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:66346000-66367000	Weak transcription	Fetal Intestine Large	intestine
29	chr7:66347000-66370000	Weak transcription	Colonic Mucosa	Colon
30	chr7:66348000-66368200	Weak transcription	Brain Germinal Matrix	brain
31	chr7:66349800-66368800	Weak transcription	NHEK	skin
32	chr7:66350600-66368400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:66350600-66385200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:66352800-66366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:66353200-66379600	Weak transcription	GM12878-XiMat	blood
36	chr7:66355200-66369000	Weak transcription	Left Ventricle	heart
37	chr7:66355600-66375400	Weak transcription	Fetal Brain Male	brain
38	chr7:66356400-66371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:66357800-66367600	Strong transcription	Liver	Liver
40	chr7:66358800-66371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:66359200-66372800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr7:66359800-66366400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:66360000-66366400	Weak transcription	Spleen	Spleen
44	chr7:66360200-66366400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:66361200-66370000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:66361200-66372600	Weak transcription	Osteobl	bone
47	chr7:66361400-66368000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:66361400-66371000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:66361600-66369000	Strong transcription	Ovary	ovary
50	chr7:66361600-66370400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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