Variant report

Variant	rs62466613
Chromosome Location	chr7:66487562-66487563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66486194..66489134-chr7:66492643..66494345,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12530524	0.94[EUR][1000 genomes]
rs12530887	0.83[EUR][1000 genomes]
rs12532995	0.80[EUR][1000 genomes]
rs12534156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534278	0.80[EUR][1000 genomes]
rs12534327	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12535023	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12536147	0.80[EUR][1000 genomes]
rs12537353	0.86[EUR][1000 genomes]
rs12537414	0.80[EUR][1000 genomes]
rs12537633	0.80[EUR][1000 genomes]
rs12538152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539202	0.88[EUR][1000 genomes]
rs12539604	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12540025	0.80[EUR][1000 genomes]
rs28867847	0.97[ASN][1000 genomes]
rs35448884	0.80[EUR][1000 genomes]
rs4717335	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4717342	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4718438	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4718450	0.80[EUR][1000 genomes]
rs62464960	0.80[EUR][1000 genomes]
rs62464964	0.91[EUR][1000 genomes]
rs62464966	0.94[EUR][1000 genomes]
rs62464967	0.86[EUR][1000 genomes]
rs62464968	0.83[EUR][1000 genomes]
rs62466591	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466592	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466594	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466596	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62466612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466618	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466620	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466625	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466629	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466630	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62466632	0.80[EUR][1000 genomes]
rs62466633	0.81[EUR][1000 genomes]
rs62466634	0.80[EUR][1000 genomes]
rs62466635	0.80[EUR][1000 genomes]
rs62466637	0.80[EUR][1000 genomes]
rs62466638	0.80[EUR][1000 genomes]
rs62466640	0.80[EUR][1000 genomes]
rs62466642	0.80[EUR][1000 genomes]
rs62466657	0.80[EUR][1000 genomes]
rs62466659	0.80[EUR][1000 genomes]
rs62468371	0.88[EUR][1000 genomes]
rs62468374	0.91[EUR][1000 genomes]
rs62468375	0.91[EUR][1000 genomes]
rs62468378	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468379	0.91[EUR][1000 genomes]
rs62468380	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468381	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468382	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62468385	0.80[EUR][1000 genomes]
rs62468402	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv981515	chr7:66477535-66532313	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv1848278	chr7:66482884-66494472	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466613	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66462400-66490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:66462400-66496000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:66462400-66500200	Weak transcription	Psoas Muscle	Psoas
4	chr7:66462400-66508000	Weak transcription	Stomach Mucosa	stomach
5	chr7:66462600-66487600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:66462600-66497200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:66462800-66494600	Weak transcription	Esophagus	oesophagus
8	chr7:66463000-66507800	Weak transcription	Fetal Brain Male	brain
9	chr7:66463200-66510000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:66470000-66489000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:66470000-66489000	Strong transcription	Fetal Intestine Small	intestine
12	chr7:66470200-66488200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr7:66470200-66488400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr7:66470200-66488400	Strong transcription	Fetal Stomach	stomach
15	chr7:66470200-66492200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr7:66470400-66488000	Strong transcription	Dnd41	blood
17	chr7:66470400-66489000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr7:66470400-66495200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:66470600-66492600	Strong transcription	Liver	Liver
20	chr7:66470600-66494800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr7:66474000-66492200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:66476800-66496800	Weak transcription	NHLF	lung
23	chr7:66477000-66495000	Weak transcription	Right Ventricle	heart
24	chr7:66477000-66499000	Weak transcription	Colonic Mucosa	Colon
25	chr7:66478000-66488200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr7:66478000-66488400	Strong transcription	Fetal Intestine Large	intestine
27	chr7:66478400-66488000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:66478400-66488000	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:66478400-66488000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr7:66478400-66490800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr7:66478800-66489800	Weak transcription	Osteobl	bone
32	chr7:66478800-66494600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:66480400-66494800	Weak transcription	Fetal Kidney	kidney
34	chr7:66480800-66494800	Weak transcription	Pancreas	Pancrea
35	chr7:66481600-66488000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:66482000-66488200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr7:66482200-66488200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:66482200-66489000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr7:66482600-66487800	Strong transcription	Lung	lung
40	chr7:66482600-66488000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr7:66482600-66488000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr7:66482600-66488800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:66482600-66488800	Strong transcription	Fetal Thymus	thymus
44	chr7:66482600-66490200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:66482800-66487800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:66482800-66488000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr7:66482800-66488000	Strong transcription	HepG2	liver
48	chr7:66482800-66489400	Strong transcription	Adipose Nuclei	Adipose
49	chr7:66483000-66488400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:66483000-66489000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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