Variant report

Variant	rs12032720
Chromosome Location	chr1:155274960-155274961
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155274302-155274998	GM19099	blood:	n/a	n/a
2	POLR2A	chr1:155274308-155274975	HepG2	liver:	n/a	n/a
3	HEY1	chr1:155274206-155275040	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155242743..155244954-chr1:155272841..155275388,3	K562	blood:
2	chr1:155270303..155273300-chr1:155273424..155278245,4	MCF-7	breast:
3	chr1:155254134..155256609-chr1:155273480..155276250,2	MCF-7	breast:
4	chr1:155242743..155244503-chr1:155272841..155275388,2	K562	blood:
5	chr1:155187979..155190547-chr1:155272522..155275143,2	K562	blood:
6	chr1:155211806..155213841-chr1:155274140..155275790,2	K562	blood:
7	chr1:155146607..155148418-chr1:155274675..155276271,2	K562	blood:
8	chr1:155246042..155249168-chr1:155274467..155279979,9	MCF-7	breast:
9	chr1:155274938..155276540-chr1:155276885..155279319,2	K562	blood:

No data

Variant related genes	Relation type
PKLR	TF binding region
FDPS	TF binding region
ENSG00000160766	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000143630	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000143627	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1052176	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1052177	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10796941	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10796943	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap]
rs10796945	0.80[CEU][hapmap];0.84[CHB][hapmap];0.82[TSI][hapmap]
rs10908461	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908462	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908463	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908465	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs10908469	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs11264349	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264352	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264353	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264354	0.86[EUR][1000 genomes]
rs11264355	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264357	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264358	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264359	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264360	0.81[AMR][1000 genomes]
rs11264361	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264367	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs11264369	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs11264371	0.84[CHB][hapmap];0.85[MEX][hapmap]
rs11264372	0.84[CHB][hapmap];0.81[MEX][hapmap]
rs11264375	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs12026638	0.89[CHB][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs12041534	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs12044063	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12049375	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067675	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12079134	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs12239114	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs12563994	0.81[ASN][1000 genomes]
rs12724079	0.84[CHB][hapmap]
rs12724449	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12749306	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1325908	0.84[CHB][hapmap]
rs1360554	0.84[CHB][hapmap]
rs1886905	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs2071053	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236863	0.81[ASN][1000 genomes]
rs2236864	0.80[AMR][1000 genomes]
rs2297480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3020781	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814318	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3814319	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4620533	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971072	0.99[ASN][1000 genomes]
rs5005770	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs6672284	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520184	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7524950	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7534795	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549276	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7554780	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177968	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8847	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932972	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9426886	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
2	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
3	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
4	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
6	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
7	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12032720	PKLR	cis	Nerve Tibial	GTEx
rs12032720	ADAM15	cis	multi-tissue	Pritchard
rs12032720	GBAP1	cis	parietal	SCAN
rs12032720	THEM5	cis	parietal	SCAN
rs12032720	SPRR2D	cis	parietal	SCAN
rs12032720	YY1AP1	cis	cerebellum	SCAN
rs12032720	RIT1	cis	cerebellum	SCAN
rs12032720	LCE1C	cis	parietal	SCAN
rs12032720	GBA	cis	Esophagus Mucosa	GTEx
rs12032720	DCST1	cis	parietal	SCAN
rs12032720	THBS3	cis	Whole Blood	GTEx
rs12032720	SPRR2A	cis	cerebellum	SCAN
rs12032720	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155265400-155277800	Weak transcription	Right Atrium	heart
2	chr1:155267800-155276000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:155270600-155275800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155270800-155278600	Weak transcription	Small Intestine	intestine
5	chr1:155271800-155275800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:155271800-155276000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155271800-155276800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:155271800-155277400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:155272600-155277800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:155273000-155275200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:155274200-155275000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:155274200-155275200	Enhancers	Colonic Mucosa	Colon
13	chr1:155274200-155275800	Flanking Active TSS	Liver	Liver
14	chr1:155274200-155276400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:155274200-155276600	Enhancers	HSMM	muscle
16	chr1:155274200-155276600	Enhancers	HSMMtube	muscle
17	chr1:155274400-155275000	Enhancers	Fetal Intestine Large	intestine
18	chr1:155274400-155275000	Enhancers	Fetal Intestine Small	intestine
19	chr1:155274400-155276800	Enhancers	Fetal Muscle Leg	muscle
20	chr1:155274600-155275400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:155274600-155275800	Enhancers	A549	lung
22	chr1:155274600-155277400	Enhancers	K562	blood
23	chr1:155274800-155275000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:155274800-155275200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:155274800-155275200	Bivalent/Poised TSS	HepG2	liver
26	chr1:155274800-155275400	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:155274800-155275800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:155274800-155276200	Enhancers	Osteobl	bone
29	chr1:155274800-155276600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:155274800-155277800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links