Variant report

Variant	rs1180086
Chromosome Location	chr9:72867579-72867580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72865927..72868229-chr9:72869161..72871391,2	MCF-7	breast:
2	chr9:72865217..72868214-chr9:72871784..72873916,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268364	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10116549	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10117899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125454	0.82[EUR][1000 genomes]
rs10126027	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780870	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780871	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs10868741	0.84[AFR][1000 genomes]
rs10868742	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868800	1.00[CHB][hapmap]
rs10868808	0.89[YRI][hapmap]
rs1112937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11141917	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142242	0.81[AFR][1000 genomes]
rs11142348	1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142363	0.96[YRI][hapmap]
rs11142365	0.93[EUR][1000 genomes]
rs11142367	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11142368	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11142370	0.96[YRI][hapmap]
rs11142371	0.82[AFR][1000 genomes]
rs11142373	0.96[YRI][hapmap]
rs11142374	0.80[AFR][1000 genomes]
rs11142375	0.88[ASN][1000 genomes]
rs11142377	1.00[CHB][hapmap]
rs11142379	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs11142380	0.93[EUR][1000 genomes]
rs11142381	0.93[EUR][1000 genomes]
rs1180079	0.88[AFR][1000 genomes]
rs1180081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1180083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180087	0.94[AFR][1000 genomes]
rs1180088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180089	1.00[CHB][hapmap]
rs1180091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180094	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]
rs1180098	0.94[AFR][1000 genomes]
rs1180099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180100	1.00[CHB][hapmap]
rs1180101	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1180103	0.88[AFR][1000 genomes]
rs1180104	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1180106	0.94[AFR][1000 genomes]
rs1180107	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1180110	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs1180111	0.96[EUR][1000 genomes]
rs1180112	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1180114	0.82[AFR][1000 genomes]
rs1180117	0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs1180118	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1180120	0.80[AFR][1000 genomes]
rs1180122	0.96[YRI][hapmap]
rs1180124	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs1180126	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1180127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180128	0.86[AFR][1000 genomes]
rs1180132	0.80[AFR][1000 genomes]
rs1180133	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs11998951	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs12006212	0.96[YRI][hapmap]
rs12115787	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12156606	1.00[YRI][hapmap]
rs12349698	0.90[AMR][1000 genomes]
rs12377677	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380844	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17051515	0.80[ASN][1000 genomes]
rs17454349	0.80[ASN][1000 genomes]
rs17454433	0.80[ASN][1000 genomes]
rs17526808	0.80[ASN][1000 genomes]
rs1887451	0.82[EUR][1000 genomes]
rs1927096	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927100	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927101	0.80[ASN][1000 genomes]
rs1927118	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1927124	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927130	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927132	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927133	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927134	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927135	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927136	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927144	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927146	0.84[YRI][hapmap]
rs1986067	0.89[ASN][1000 genomes]
rs2026137	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2148857	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148863	0.82[EUR][1000 genomes]
rs2148866	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148867	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182734	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182737	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182738	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182741	1.00[ASN][1000 genomes]
rs2309634	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309645	1.00[CHB][hapmap]
rs2479033	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2768644	0.88[AFR][1000 genomes]
rs2768645	0.93[AFR][1000 genomes]
rs2768646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2773362	0.88[AFR][1000 genomes]
rs2773363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871293	0.96[YRI][hapmap]
rs4384045	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449855	0.96[YRI][hapmap]
rs4744591	0.92[AFR][1000 genomes]
rs4744989	0.92[AMR][1000 genomes]
rs4744993	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744999	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019539	0.80[ASN][1000 genomes]
rs58720670	0.82[AFR][1000 genomes]
rs6560015	0.80[ASN][1000 genomes]
rs6560016	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560018	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.92[ASN][1000 genomes]
rs66756859	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs68171482	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024117	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024812	0.80[ASN][1000 genomes]
rs7034322	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7043171	1.00[CHB][hapmap]
rs7047789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73454795	0.82[AFR][1000 genomes]
rs7852005	0.82[AFR][1000 genomes]
rs7853298	0.82[EUR][1000 genomes]
rs7854735	0.84[AFR][1000 genomes]
rs7858988	0.96[YRI][hapmap]
rs7860729	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7868564	0.92[AFR][1000 genomes]
rs7869429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871674	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs943534	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[CHB][hapmap]
rs943536	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs943540	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72845000-72870400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:72847400-72870800	Weak transcription	Pancreas	Pancrea
3	chr9:72855800-72870800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:72856000-72867600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:72860600-72870800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:72865800-72869200	Weak transcription	Liver	Liver
7	chr9:72867200-72868400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr9:72867400-72867600	Enhancers	Brain Angular Gyrus	brain
9	chr9:72867400-72868000	Enhancers	Brain Substantia Nigra	brain
10	chr9:72867400-72868200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:72867400-72868200	Enhancers	K562	blood

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