Variant report

Variant	rs9487342
Chromosome Location	chr6:110607412-110607413
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110606982..110609095-chr6:110619308..110622290,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11750973	0.92[EUR][1000 genomes]
rs11752726	0.81[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs11753218	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs11753379	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11756892	0.85[EUR][1000 genomes]
rs11757487	0.92[EUR][1000 genomes]
rs12111403	0.81[GIH][hapmap];0.92[TSI][hapmap]
rs17071335	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17071340	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17071348	0.92[EUR][1000 genomes]
rs17071350	0.92[EUR][1000 genomes]
rs17071361	0.92[EUR][1000 genomes]
rs17071363	0.92[EUR][1000 genomes]
rs17071364	0.92[EUR][1000 genomes]
rs17071372	0.92[EUR][1000 genomes]
rs17071377	0.92[EUR][1000 genomes]
rs17071379	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17071380	0.95[EUR][1000 genomes]
rs17071382	0.95[EUR][1000 genomes]
rs17071389	0.95[EUR][1000 genomes]
rs17071391	0.95[EUR][1000 genomes]
rs17071401	0.95[EUR][1000 genomes]
rs2334320	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2334324	0.95[EUR][1000 genomes]
rs2878175	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs2878176	0.80[EUR][1000 genomes]
rs4516983	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs55842731	0.92[EUR][1000 genomes]
rs56241136	0.92[EUR][1000 genomes]
rs57228333	1.00[EUR][1000 genomes]
rs59987321	0.92[EUR][1000 genomes]
rs6910958	0.95[EUR][1000 genomes]
rs6931749	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs73763003	0.92[EUR][1000 genomes]
rs73763004	0.92[EUR][1000 genomes]
rs73763005	0.92[EUR][1000 genomes]
rs73763006	0.92[EUR][1000 genomes]
rs73765680	0.85[EUR][1000 genomes]
rs73765683	0.90[EUR][1000 genomes]
rs73765685	0.92[EUR][1000 genomes]
rs73765687	0.92[EUR][1000 genomes]
rs73765690	0.92[EUR][1000 genomes]
rs73765691	0.92[EUR][1000 genomes]
rs73765692	0.82[EUR][1000 genomes]
rs7741277	0.92[EUR][1000 genomes]
rs7746806	0.87[EUR][1000 genomes]
rs7750037	0.81[GIH][hapmap];0.92[TSI][hapmap]
rs7754242	0.95[EUR][1000 genomes]
rs7756496	0.92[EUR][1000 genomes]
rs7756509	0.92[EUR][1000 genomes]
rs7758018	0.84[EUR][1000 genomes]
rs7758053	0.92[EUR][1000 genomes]
rs7760856	0.92[EUR][1000 genomes]
rs7770311	0.92[EUR][1000 genomes]
rs7770706	0.95[EUR][1000 genomes]
rs7771030	0.95[EUR][1000 genomes]
rs7771378	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7771574	0.95[EUR][1000 genomes]
rs7774900	0.92[EUR][1000 genomes]
rs9481052	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9487340	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9487343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9487348	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][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	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv949643	chr6:110537685-110889332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1847660	chr6:110606987-110985314	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110550600-110608200	Weak transcription	Fetal Kidney	kidney
2	chr6:110600200-110608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:110604800-110609000	Weak transcription	Pancreas	Pancrea
4	chr6:110605000-110617400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:110605200-110607600	Weak transcription	Aorta	Aorta
6	chr6:110605400-110608400	Weak transcription	HepG2	liver
7	chr6:110605400-110617200	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:110605800-110609400	Enhancers	Stomach Mucosa	stomach
9	chr6:110606600-110608000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:110606800-110612400	Weak transcription	Ovary	ovary
11	chr6:110607000-110608400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:110607000-110608600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:110607000-110608800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:110607000-110608800	Weak transcription	Brain Anterior Caudate	brain
15	chr6:110607000-110608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:110607200-110608000	Enhancers	Esophagus	oesophagus
17	chr6:110607200-110608000	Strong transcription	Fetal Stomach	stomach
18	chr6:110607400-110607600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:110607400-110608800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:110607400-110610200	Strong transcription	Stomach Smooth Muscle	stomach

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