Variant report

Variant	rs12067005
Chromosome Location	chr1:93543119-93543120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93542830..93545559-chr20:45984443..45987122,2	MCF-7	breast:
2	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
3	chr1:93543004..93547588-chr1:93644888..93649088,6	K562	blood:
4	chr1:93497881..93500258-chr1:93541751..93544329,2	K562	blood:
5	chr1:93296076..93299049-chr1:93541677..93546567,5	K562	blood:
6	chr1:93314734..93317720-chr1:93541200..93543967,2	K562	blood:

Variant related genes	Relation type
ENSG00000117500	Chromatin interaction
ENSG00000122406	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10874765	0.95[YRI][hapmap]
rs11164874	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164878	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11164882	0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11586323	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12057476	0.91[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12064785	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12066315	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12070900	0.89[YRI][hapmap]
rs12085959	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs12087466	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12088338	0.81[EUR][1000 genomes]
rs12094547	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1414367	0.91[ASW][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17131699	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2391227	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2484485	0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2749735	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2783492	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2783498	0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs2783506	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2815408	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2815409	0.91[ASW][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2815410	0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2815411	0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2815412	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2815414	0.81[EUR][1000 genomes]
rs36057148	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs504810	0.91[CEU][hapmap]
rs505531	0.82[EUR][1000 genomes]
rs506556	0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs519723	0.96[TSI][hapmap]
rs522999	0.81[CEU][hapmap]
rs546	0.91[ASW][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55701931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs571212	0.92[TSI][hapmap]
rs573056	0.96[TSI][hapmap]
rs629153	0.95[YRI][hapmap]
rs633789	0.92[TSI][hapmap]
rs658178	0.95[YRI][hapmap]
rs6667701	0.96[TSI][hapmap]
rs667680	0.82[AFR][1000 genomes]
rs668944	0.96[TSI][hapmap]
rs671559	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71510760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs797660	0.82[AFR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs12067005	RP4-717I23.3	cis	Whole Blood	GTEx
rs12067005	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12067005	HSS00001365	cis	multi-tissue	Pritchard
rs12067005	RP4-717I23.3	cis	Artery Tibial	GTEx
rs12067005	F3	cis	parietal	SCAN
rs12067005	DR1	cis	multi-tissue	Pritchard
rs12067005	RP4-717I23.3	cis	Stomach	GTEx
rs12067005	LOC646848	cis	normal skin	skin_eQTL
rs12067005	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs12067005	LOC646848	cis	multi-tissue	Pritchard
rs12067005	RP4-717I23.3	cis	Thyroid	GTEx
rs12067005	RP4-717I23.3	cis	Artery Aorta	GTEx
rs12067005	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12067005	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs12067005	TMED5	cis	parietal	SCAN
rs12067005	RP4-717I23.3	cis	lung	GTEx
rs12067005	RWDD3	cis	parietal	SCAN
rs12067005	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12067005	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12067005	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs12067005	TMED5	cis	multi-tissue	Pritchard
rs12067005	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12067005	TMED5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93538200-93543800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:93539400-93543800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:93541200-93543600	Weak transcription	Stomach Mucosa	stomach
4	chr1:93541200-93543800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:93541400-93544200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:93541800-93544000	Enhancers	HepG2	liver
7	chr1:93542200-93543600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:93542400-93543200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr1:93542400-93544000	Enhancers	Fetal Intestine Small	intestine
10	chr1:93542600-93543200	Enhancers	Fetal Intestine Large	intestine
11	chr1:93542600-93544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:93542600-93544000	Weak transcription	Colonic Mucosa	Colon
13	chr1:93542800-93543800	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:93542800-93544000	Enhancers	Fetal Thymus	thymus
15	chr1:93543000-93543400	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:93543000-93543800	Enhancers	K562	blood

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