Variant report

Variant	rs12540695
Chromosome Location	chr7:66453577-66453578
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66451976..66454311-chr7:66458213..66459754,2	K562	blood:
2	chr7:66453405..66455098-chr7:66455519..66457456,2	MCF-7	breast:
3	chr7:66449461..66454980-chr7:66457220..66462076,6	K562	blood:

Variant related genes	Relation type
ENSG00000126524	Chromatin interaction
ENSG00000198874	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs12531516	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12532160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532307	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12532995	1.00[CEU][hapmap]
rs12533830	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12534278	0.87[AMR][1000 genomes]
rs12534401	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535023	0.87[AMR][1000 genomes]
rs12535268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12537353	0.87[AMR][1000 genomes]
rs12537414	0.87[AMR][1000 genomes]
rs12537825	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12537955	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12539366	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12539604	0.81[AMR][1000 genomes]
rs17567255	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2091314	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2293351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34758320	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35448884	0.87[AMR][1000 genomes]
rs3778911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3800819	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717323	0.81[AMR][1000 genomes]
rs4717329	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs4717332	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717335	0.81[AMR][1000 genomes]
rs4718426	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4718434	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718438	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs4718450	0.87[AMR][1000 genomes]
rs62465700	0.81[AMR][1000 genomes]
rs62465701	0.81[AMR][1000 genomes]
rs62465705	0.81[AMR][1000 genomes]
rs62465734	0.87[AMR][1000 genomes]
rs62465736	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465738	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465739	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465740	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465741	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465742	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465743	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465744	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465745	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62465747	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465748	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465750	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62465752	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62466575	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62466578	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62466582	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62466584	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62466586	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62466588	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62466589	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62466591	0.81[AMR][1000 genomes]
rs62466592	0.81[AMR][1000 genomes]
rs62466594	0.81[AMR][1000 genomes]
rs62466596	0.81[AMR][1000 genomes]
rs62466632	0.87[AMR][1000 genomes]
rs62466633	0.87[AMR][1000 genomes]
rs62466634	0.87[AMR][1000 genomes]
rs62466635	0.87[AMR][1000 genomes]
rs62466637	0.87[AMR][1000 genomes]
rs62466638	0.87[AMR][1000 genomes]
rs62466639	0.87[AMR][1000 genomes]
rs62466640	0.87[AMR][1000 genomes]
rs62466642	0.87[AMR][1000 genomes]
rs62466657	0.87[AMR][1000 genomes]
rs62466659	0.87[AMR][1000 genomes]
rs62468374	0.87[AMR][1000 genomes]
rs62468375	0.87[AMR][1000 genomes]
rs62468378	0.87[AMR][1000 genomes]
rs62468379	0.87[AMR][1000 genomes]
rs62468380	0.87[AMR][1000 genomes]
rs62468381	0.87[AMR][1000 genomes]
rs62468382	0.87[AMR][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	nsv966836	chr7:66438146-66457576	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12540695	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12540695	RABGEF1	cis	lymphoblastoid	seeQTL
rs12540695	RABGEF1	cis	multi-tissue	Pritchard
rs12540695	hmm32897	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66420600-66459200	Weak transcription	Psoas Muscle	Psoas
2	chr7:66433200-66458600	Weak transcription	Right Atrium	heart
3	chr7:66444800-66456800	Weak transcription	Stomach Mucosa	stomach
4	chr7:66446200-66453600	Weak transcription	Fetal Intestine Small	intestine
5	chr7:66446600-66459400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:66449400-66459200	Weak transcription	HepG2	liver
7	chr7:66449600-66459400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:66449800-66453600	Weak transcription	Fetal Stomach	stomach
9	chr7:66450200-66455200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:66450200-66456800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:66450400-66456800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:66450600-66456800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:66450800-66458200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:66451200-66456800	Weak transcription	Primary B cells from cord blood	blood
15	chr7:66451400-66455800	Weak transcription	Thymus	Thymus
16	chr7:66451600-66454400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:66451600-66455200	Weak transcription	A549	lung
18	chr7:66451600-66455800	Strong transcription	HSMM	muscle
19	chr7:66451600-66458600	Strong transcription	Fetal Thymus	thymus
20	chr7:66451600-66458800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:66451600-66458800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:66451600-66459200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:66451600-66459400	Weak transcription	Esophagus	oesophagus
24	chr7:66451800-66454200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:66451800-66456800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:66451800-66458200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:66451800-66458400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:66451800-66458600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:66451800-66458600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr7:66451800-66458600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:66451800-66458800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:66451800-66459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:66451800-66459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr7:66452000-66458200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:66452000-66458400	Strong transcription	Adipose Nuclei	Adipose
36	chr7:66452000-66458600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:66452000-66458600	Strong transcription	Liver	Liver
38	chr7:66452000-66458800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:66452000-66459200	Weak transcription	Aorta	Aorta
40	chr7:66452000-66459800	Weak transcription	Small Intestine	intestine
41	chr7:66452200-66454000	Strong transcription	Brain Anterior Caudate	brain
42	chr7:66452200-66454800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:66452200-66456800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr7:66452200-66457800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:66452200-66458000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr7:66452200-66458600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:66452200-66458800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:66452200-66458800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:66452200-66458800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr7:66452200-66459000	Weak transcription	Fetal Brain Male	brain

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