Variant report

Variant	rs12684427
Chromosome Location	chr9:96723803-96723804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96656015..96657684-chr9:96723768..96726547,2	MCF-7	breast:
2	chr9:96712713..96719267-chr9:96721537..96727951,10	MCF-7	breast:
3	chr9:96444241..96444748-chr9:96723455..96724298,2	MCF-7	breast:
4	chr9:96722430..96724465-chr9:96726832..96729189,2	K562	blood:
5	chr9:96445904..96447979-chr9:96722570..96724839,2	MCF-7	breast:
6	chr9:96720222..96721910-chr9:96722308..96724040,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131668	Chromatin interaction
ENSG00000235601	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10117457	0.86[EUR][1000 genomes]
rs10122334	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs10123954	0.87[EUR][1000 genomes]
rs10429556	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10429603	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10435922	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10435924	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739967	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739969	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs10761308	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761309	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10761313	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761315	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs10821284	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821285	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10993037	0.82[EUR][1000 genomes]
rs10993058	0.81[CEU][hapmap]
rs12351292	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1320547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331216	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1331217	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1331218	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1331219	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1343995	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1360429	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1411860	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1418251	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs1576640	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1590969	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1592153	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1832857	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1854835	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1933667	0.80[EUR][1000 genomes]
rs1933668	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1933669	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1933679	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026917	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2094927	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2150625	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153058	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2153070	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153792	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2211362	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2225458	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2226117	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3847307	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs3996241	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4282631	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744308	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744310	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744316	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs6479522	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479527	0.81[CEU][hapmap]
rs6479528	0.81[CEU][hapmap]
rs7033481	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7033898	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7045643	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7858069	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7867253	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7867925	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs914295	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs914296	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs914297	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9299414	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs987511	0.95[EUR][1000 genomes];0.95[ASN][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	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96720400-96724400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:96721200-96724200	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr9:96722000-96724000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:96722800-96724200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:96723000-96724000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr9:96723000-96724400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:96723000-96725800	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr9:96723000-96728800	Weak transcription	Pancreas	Pancrea
9	chr9:96723000-96729800	Weak transcription	Gastric	stomach
10	chr9:96723200-96724200	Bivalent Enhancer	Fetal Stomach	stomach
11	chr9:96723200-96725400	Enhancers	Hela-S3	cervix
12	chr9:96723400-96724000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell

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