Variant report

Variant	rs12538724
Chromosome Location	chr7:66481250-66481251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12530524	0.92[EUR][1000 genomes]
rs12530887	0.81[EUR][1000 genomes]
rs12532160	1.00[CEU][hapmap]
rs12532995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12534156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534327	0.83[ASN][1000 genomes]
rs12535023	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12537353	0.83[EUR][1000 genomes]
rs12538152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539202	0.86[EUR][1000 genomes]
rs12539604	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12540695	1.00[CEU][hapmap]
rs28867847	0.97[ASN][1000 genomes]
rs4717335	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4717342	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4718438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62464964	0.89[EUR][1000 genomes]
rs62464966	0.92[EUR][1000 genomes]
rs62464967	0.83[EUR][1000 genomes]
rs62464968	0.81[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466618	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466620	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466625	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62466629	0.83[ASN][1000 genomes]
rs62466630	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62468371	0.86[EUR][1000 genomes]
rs62468374	0.89[EUR][1000 genomes]
rs62468375	0.89[EUR][1000 genomes]
rs62468378	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468379	0.89[EUR][1000 genomes]
rs62468380	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468381	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62468382	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12538724	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12538724	RABGEF1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66462200-66482600	Weak transcription	Aorta	Aorta
2	chr7:66462400-66482200	Weak transcription	Small Intestine	intestine
3	chr7:66462400-66482600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:66462400-66490000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:66462400-66496000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:66462400-66500200	Weak transcription	Psoas Muscle	Psoas
7	chr7:66462400-66508000	Weak transcription	Stomach Mucosa	stomach
8	chr7:66462600-66482800	Weak transcription	NHEK	skin
9	chr7:66462600-66484600	Weak transcription	HUVEC	blood vessel
10	chr7:66462600-66487600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:66462600-66497200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:66462800-66494600	Weak transcription	Esophagus	oesophagus
13	chr7:66463000-66487200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:66463000-66507800	Weak transcription	Fetal Brain Male	brain
15	chr7:66463200-66482600	Weak transcription	HMEC	breast
16	chr7:66463200-66483000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:66463200-66484800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:66463200-66487400	Weak transcription	NH-A	brain
19	chr7:66463200-66510000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:66468600-66484400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:66469000-66484400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:66469200-66482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:66470000-66489000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:66470000-66489000	Strong transcription	Fetal Intestine Small	intestine
25	chr7:66470200-66488200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:66470200-66488400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:66470200-66488400	Strong transcription	Fetal Stomach	stomach
28	chr7:66470200-66492200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr7:66470400-66484400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:66470400-66488000	Strong transcription	Dnd41	blood
31	chr7:66470400-66489000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr7:66470400-66495200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:66470600-66485400	Strong transcription	Placenta	Placenta
34	chr7:66470600-66492600	Strong transcription	Liver	Liver
35	chr7:66470600-66494800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:66470800-66481600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:66472400-66481600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:66472400-66484600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:66472400-66485400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:66472600-66483400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:66472600-66487000	Weak transcription	A549	lung
42	chr7:66472800-66484400	Weak transcription	Hela-S3	cervix
43	chr7:66473600-66484000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:66474000-66492200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:66474600-66484800	Weak transcription	HSMM	muscle
46	chr7:66474600-66484800	Weak transcription	HSMMtube	muscle
47	chr7:66475200-66485600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr7:66475400-66481400	Strong transcription	Adipose Nuclei	Adipose
49	chr7:66476000-66482800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:66476000-66486600	Strong transcription	Left Ventricle	heart

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