Variant report

Variant	rs7427935
Chromosome Location	chr3:89158550-89158551
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	chr3:89158394..89160004-chr3:89161963..89163485,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11128070	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494816	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13077331	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13434229	0.91[EUR][1000 genomes]
rs56895676	0.93[EUR][1000 genomes]
rs57618914	0.93[EUR][1000 genomes]
rs58716947	0.91[EUR][1000 genomes]
rs58987133	0.93[EUR][1000 genomes]
rs59083916	0.91[EUR][1000 genomes]
rs59111523	0.93[EUR][1000 genomes]
rs59800917	0.93[EUR][1000 genomes]
rs60573712	0.91[EUR][1000 genomes]
rs61000929	0.91[EUR][1000 genomes]
rs61253060	0.93[EUR][1000 genomes]
rs6551398	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551406	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767230	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779710	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790662	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67935343	0.83[EUR][1000 genomes]
rs6793981	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800287	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6804377	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6807840	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7373480	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73845930	0.93[EUR][1000 genomes]
rs73845931	0.93[EUR][1000 genomes]
rs73845942	0.91[EUR][1000 genomes]
rs73845947	0.93[EUR][1000 genomes]
rs73845948	0.93[EUR][1000 genomes]
rs7426466	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7426527	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7427745	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs7622368	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632543	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633559	0.82[JPT][hapmap]
rs7651124	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9310108	0.83[AMR][1000 genomes]
rs9810701	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811026	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9814718	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9815137	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828822	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9834135	0.85[ASN][1000 genomes]
rs9835264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9859735	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860030	1.00[CEU][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]
rs9861649	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868041	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883722	1.00[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89156000-89158800	Active TSS	Brain Germinal Matrix	brain
2	chr3:89156000-89159600	Active TSS	Fetal Brain Male	brain
3	chr3:89156000-89159800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:89156200-89158600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:89156200-89159200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:89157600-89159000	Active TSS	Fetal Muscle Leg	muscle
7	chr3:89157600-89159200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr3:89157600-89163000	Active TSS	Fetal Brain Female	brain
9	chr3:89157600-89163200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:89157600-89163200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:89157600-89163200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:89157600-89163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:89157600-89163600	Weak transcription	Spleen	Spleen
14	chr3:89157800-89163000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:89158000-89159000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:89158000-89163200	Weak transcription	Fetal Heart	heart
17	chr3:89158200-89159600	Weak transcription	Right Atrium	heart
18	chr3:89158200-89162400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:89158200-89163000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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