Variant report

Variant	rs9425483
Chromosome Location	chr1:180096149-180096150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:180096052-180096288	K562	blood:	n/a	chr1:180096173-180096180 chr1:180096173-180096181 chr1:180096172-180096182 chr1:180096173-180096181
2	MYC	chr1:180095948-180096157	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:180096060-180096224	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr1:180096045-180096346	K562	blood:	n/a	n/a
5	STAT3	chr1:180095889-180096293	MCF10A-Er-Src	breast:	n/a	n/a
6	TAL1	chr1:180096007-180096327	K562	blood:	n/a	n/a
7	FOS	chr1:180095941-180096358	MCF10A-Er-Src	breast:	n/a	chr1:180096173-180096180 chr1:180096173-180096181 chr1:180096172-180096182 chr1:180096173-180096181
8	STAT3	chr1:180095936-180096262	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr1:180095660-180096269	T-47D	breast:	n/a	chr1:180096173-180096180 chr1:180096173-180096181 chr1:180096172-180096182 chr1:180096173-180096181
10	EP300	chr1:180095773-180096185	T-47D	breast:	n/a	n/a
11	TEAD4	chr1:180095946-180096260	K562	blood:	n/a	n/a
12	FOXA1	chr1:180095675-180096182	T-47D	breast:	n/a	chr1:180095917-180095932
13	TEAD4	chr1:180095974-180096349	K562	blood:	n/a	n/a
14	MAFK	chr1:180096087-180096290	K562	blood:	n/a	chr1:180096173-180096183
15	STAT3	chr1:180095900-180096342	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr1:180095995-180096195	K562	blood:	n/a	n/a
17	FOS	chr1:180095948-180096348	MCF10A-Er-Src	breast:	n/a	chr1:180096173-180096180 chr1:180096173-180096181 chr1:180096172-180096182 chr1:180096173-180096181
18	FOS	chr1:180096005-180096337	MCF10A-Er-Src	breast:	n/a	chr1:180096173-180096180 chr1:180096173-180096181 chr1:180096172-180096182 chr1:180096173-180096181
19	TCF7L2	chr1:180095900-180096220	PANC-1	pancreas:	n/a	chr1:180096172-180096181
20	FOXA1	chr1:180095738-180096151	T-47D	breast:	n/a	chr1:180095917-180095932
21	FOS	chr1:180095928-180096350	MCF10A-Er-Src	breast:	n/a	chr1:180096173-180096180 chr1:180096173-180096181 chr1:180096172-180096182 chr1:180096173-180096181
22	EP300	chr1:180096086-180096259	K562	blood:	n/a	n/a
23	GATA3	chr1:180095686-180096210	T-47D	breast:	n/a	n/a
24	E2F4	chr1:180096142-180096255	MCF10A-Er-Src	breast:	n/a	n/a
25	MAFK	chr1:180095974-180096237	HepG2	liver:	n/a	chr1:180096173-180096183
26	ATF1	chr1:180095935-180096214	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179849546..179851570-chr1:180093822..180096311,2	K562	blood:
2	chr1:180095863..180097872-chr1:180124437..180126586,3	MCF-7	breast:
3	chr1:179922333..179925402-chr1:180094478..180098472,3	K562	blood:
4	chr1:180095534..180097819-chr1:180123272..180124812,2	K562	blood:
5	chr1:180094856..180097003-chr1:180124933..180127557,2	K562	blood:
6	chr1:180094467..180097034-chr1:180123312..180125749,2	K562	blood:
7	chr1:180095809..180098718-chr1:180115935..180118592,2	K562	blood:
8	chr1:180094976..180098396-chr1:180099565..180103492,4	MCF-7	breast:
9	chr1:180094624..180096269-chr1:180125316..180126971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261817	TF binding region
ENSG00000260360	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10753206	0.86[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10798730	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10798732	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10913916	0.83[CEU][hapmap]
rs10913931	0.91[ASN][1000 genomes]
rs12040314	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12040376	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12080763	0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1981314	0.83[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2319773	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2477119	0.81[CEU][hapmap]
rs2501621	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs3767201	0.83[CEU][hapmap]
rs4263962	0.83[CEU][hapmap]
rs4336810	0.92[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4506429	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4651055	0.83[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs4651057	0.87[AFR][1000 genomes]
rs4652464	0.85[EUR][1000 genomes]
rs4652471	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4652472	0.91[ASN][1000 genomes]
rs4652473	0.89[ASN][1000 genomes]
rs4652475	0.86[ASN][1000 genomes]
rs528350	0.82[CHD][hapmap]
rs6425609	0.88[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6659911	0.83[EUR][1000 genomes]
rs6660984	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6691060	0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6691435	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6692394	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7544467	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7545835	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7551181	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425485	0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425486	0.91[ASN][1000 genomes]
rs9425489	0.88[ASN][1000 genomes]
rs9425857	0.84[EUR][1000 genomes]
rs9425858	0.84[EUR][1000 genomes]
rs9425859	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs9425863	0.91[ASN][1000 genomes]
rs9425866	0.88[ASN][1000 genomes]
rs9425868	0.92[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9887843	0.83[EUR][1000 genomes]

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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9425483	MRPS14	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180086600-180100800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:180086600-180102400	Weak transcription	Pancreas	Pancrea
3	chr1:180087000-180097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:180087200-180097000	Weak transcription	Lung	lung
5	chr1:180087200-180097400	Weak transcription	Esophagus	oesophagus
6	chr1:180089200-180097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:180093000-180096200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:180094600-180098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:180095200-180100200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:180095400-180096600	Enhancers	NHEK	skin
11	chr1:180095600-180096400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:180095600-180096400	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:180095600-180096400	Enhancers	Fetal Intestine Small	intestine
14	chr1:180095600-180096400	Enhancers	K562	blood
15	chr1:180095600-180096600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:180095600-180097400	Enhancers	Stomach Mucosa	stomach
17	chr1:180095800-180096200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:180095800-180096400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:180095800-180096400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:180095800-180096400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:180095800-180096400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:180095800-180096600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:180096000-180096200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:180096000-180096400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:180096000-180096400	Enhancers	H9 Cell Line	embryonic stem cell
26	chr1:180096000-180096400	Enhancers	Primary T cells from cord blood	blood
27	chr1:180096000-180096400	Enhancers	Fetal Intestine Large	intestine
28	chr1:180096000-180097200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:180096000-180099600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:180096000-180102400	Enhancers	Primary monocytes fromperipheralblood	blood

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