Variant report

Variant	rs9425485
Chromosome Location	chr1:180099587-180099588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180098705..180101372-chr1:180105512..180107387,2	MCF-7	breast:
2	chr1:180097925..180100588-chr1:180122221..180125022,3	MCF-7	breast:
3	chr1:180086567..180088551-chr1:180097799..180100579,2	K562	blood:
4	chr1:180098168..180100831-chr1:180111412..180113177,2	K562	blood:
5	chr1:180097218..180099611-chr1:180115672..180117435,2	K562	blood:
6	chr1:180094976..180098396-chr1:180099565..180103492,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116260	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10753206	0.82[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798729	0.81[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10798730	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913917	0.88[CEU][hapmap]
rs10913927	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10913931	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12027335	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12040314	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040376	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080763	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1297205	0.80[CEU][hapmap]
rs2477112	0.88[CEU][hapmap]
rs2477116	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2477118	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2477120	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2501607	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2501610	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2501611	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2501613	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2501615	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2501616	0.82[EUR][1000 genomes]
rs2501617	0.81[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs2762859	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs3753814	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs3767200	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3767202	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818999	0.84[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3930305	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4076449	0.88[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4147169	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4256775	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4336810	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4506429	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4651054	0.81[EUR][1000 genomes]
rs4651057	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4652462	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4652463	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4652465	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4652470	0.81[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs4652471	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652472	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652473	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652475	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs483307	0.88[CEU][hapmap]
rs500371	0.80[CEU][hapmap]
rs510209	0.88[CEU][hapmap]
rs528350	0.81[CEU][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs534168	0.81[CEU][hapmap]
rs6425603	0.88[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6425609	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6657347	0.88[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6691060	0.81[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691435	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7524849	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7525385	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7528811	0.82[ASW][hapmap];0.81[CEU][hapmap]
rs7548486	0.84[EUR][1000 genomes]
rs7551181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9286932	0.88[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9425481	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9425482	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9425483	0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425486	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425489	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425849	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9425851	0.84[EUR][1000 genomes]
rs9425854	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9425855	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425856	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425860	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425861	0.84[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9425863	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425866	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425868	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9425485	ASTN1	cis	parietal	SCAN
rs9425485	ASTN1	cis	cerebellum	SCAN

Chromatin state (count:12 , 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	chr1:180095200-180100200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr1:180096000-180099600	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr1:180096000-180102400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:180096400-180099800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:180096400-180100800	Weak transcription	K562	blood
8	chr1:180096600-180100800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:180097600-180099800	Weak transcription	Primary B cells from cord blood	blood
10	chr1:180098800-180099800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:180098800-180100200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:180099400-180103800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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