Variant report

Variant	rs12120152
Chromosome Location	chr1:171723809-171723810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr1:171722890-171723879	K562	blood:	n/a	n/a
2	CTCF	chr1:171723660-171723810	NHEK	skin:	n/a	n/a
3	CTCF	chr1:171723660-171723810	AG10803	skin:	n/a	n/a
4	POLR2A	chr1:171722769-171728047	K562	blood:	n/a	n/a
5	POLR2A	chr1:171723712-171723810	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171722184..171727474-chr1:171729363..171734018,7	K562	blood:
2	chr1:171714902..171716862-chr1:171721473..171724148,2	K562	blood:
3	chr1:171710699..171713555-chr1:171719677..171724483,6	MCF-7	breast:
4	chr1:171723775..171729031-chr1:171729363..171735304,8	K562	blood:
5	chr1:171721245..171723879-chr1:171723986..171725815,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232261	TF binding region
ENSG00000271459	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10798598	0.93[EUR][1000 genomes]
rs10798599	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10798603	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10913508	0.93[EUR][1000 genomes]
rs10913530	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10913559	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10913578	0.89[YRI][hapmap]
rs10913586	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583530	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11805692	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11806314	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12045452	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12096984	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12139610	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16843251	0.86[YRI][hapmap]
rs2073484	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2227229	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3753539	0.89[YRI][hapmap]
rs4342884	0.82[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4468194	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6425400	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6662836	0.95[CEU][hapmap]
rs6665581	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668623	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6672082	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673782	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674468	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674688	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6674774	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6682452	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6685742	0.90[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6688447	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6700606	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap]
rs763225	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9659578	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs9943293	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs999685	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12120152	DNM3	cis	cerebellum	SCAN
rs12120152	METTL13	cis	parietal	SCAN
rs12120152	VAMP4	cis	multi-tissue	Pritchard
rs12120152	PRDX6	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171720800-171724800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:171721000-171725600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:171722200-171724800	Enhancers	NHLF	lung
4	chr1:171722800-171724200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:171722800-171724200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:171722800-171724200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:171722800-171724200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:171722800-171724400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:171722800-171724400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:171722800-171724400	Enhancers	HSMM	muscle
11	chr1:171722800-171724600	Enhancers	HMEC	breast
12	chr1:171722800-171724800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:171723000-171724000	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:171723000-171724000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:171723000-171724000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:171723000-171724000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:171723000-171724200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:171723000-171724200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:171723000-171724200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:171723000-171724200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:171723000-171724200	Flanking Active TSS	HSMMtube	muscle
22	chr1:171723000-171724200	Enhancers	Osteobl	bone
23	chr1:171723000-171724600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:171723000-171724800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:171723200-171724000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:171723200-171724000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:171723200-171724000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:171723200-171724200	Enhancers	NH-A	brain
29	chr1:171723200-171724200	Flanking Active TSS	NHEK	skin
30	chr1:171723200-171724400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:171723200-171724400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:171723400-171724000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:171723400-171724600	Enhancers	Lung	lung
34	chr1:171723600-171724000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:171723600-171724400	Enhancers	NHDF-Ad	bronchial
36	chr1:171723600-171730200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:171723800-171724200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:171723800-171724200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:171723800-171724200	Enhancers	K562	blood
40	chr1:171723800-171724400	Enhancers	GM12878-XiMat	blood
41	chr1:171723800-171724600	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links