Variant report

Variant	rs4642091
Chromosome Location	chr3:111489842-111489843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10934102	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs10934103	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs13071304	0.96[EUR][1000 genomes]
rs13085147	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs13090883	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs17423699	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs17424287	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs34307743	0.88[EUR][1000 genomes]
rs34444935	0.88[EUR][1000 genomes]
rs3922703	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs3922705	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs4234402	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs4234403	0.89[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234405	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs4308247	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs4349472	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs4373040	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4405880	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4416359	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs4429600	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs4438630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4546124	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs4645114	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs4682058	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682059	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682060	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682062	0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs4682304	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682306	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682307	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682308	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682309	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4682311	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs4682315	0.94[EUR][1000 genomes]
rs6438005	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs66499316	0.94[EUR][1000 genomes]
rs6762439	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763624	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs6768626	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs6777540	0.83[YRI][hapmap]
rs6777990	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6780845	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6782894	0.89[CEU][hapmap]
rs6786443	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs6791845	0.89[CEU][hapmap]
rs6804906	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6807045	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68097220	0.98[EUR][1000 genomes]
rs7632963	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7633037	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7637178	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640556	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7641533	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9288929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9631450	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850851	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968124	0.92[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr3:111480200-111492000	Enhancers	Liver	Liver
2	chr3:111486800-111490000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:111487200-111490000	Enhancers	Fetal Muscle Leg	muscle
4	chr3:111487800-111493000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:111487800-111521000	Weak transcription	Gastric	stomach
6	chr3:111488000-111493000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:111488000-111493400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:111488000-111501400	Weak transcription	Psoas Muscle	Psoas
9	chr3:111488400-111490000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:111488400-111496800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:111489000-111495200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:111489200-111492400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:111489200-111492400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:111489400-111492400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:111489400-111500600	Weak transcription	Fetal Lung	lung
16	chr3:111489600-111490400	Enhancers	Fetal Muscle Trunk	muscle
17	chr3:111489800-111490000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:111489800-111490000	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:111489800-111490400	Enhancers	Pancreas	Pancrea

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