Variant report

Variant	rs4341641
Chromosome Location	chr13:38189454-38189455
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1003062	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10161932	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1041019	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535775	0.82[CEU][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1570612	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs17056378	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1886165	0.88[CEU][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1924296	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1924306	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1951894	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977278	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2025405	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28407779	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812842	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4368050	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943523	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7319022	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7319663	0.83[EUR][1000 genomes]
rs7320832	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330467	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7335776	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7336380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338118	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs7338244	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7984226	0.87[CEU][hapmap]
rs7996934	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs8000496	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8001321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315504	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532087	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9547970	1.00[CHB][hapmap]
rs9566239	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576302	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576310	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576319	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576320	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603225	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603240	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603241	0.88[CEU][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603247	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1038850	chr13:37820489-38209571	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv832583	chr13:38030752-38202000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv430553	chr13:38184100-38203200	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38177000-38190400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr13:38188400-38189800	Weak transcription	NHDF-Ad	bronchial
3	chr13:38189000-38189800	Enhancers	NHEK	skin
4	chr13:38189200-38191000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr13:38189200-38192400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:38189400-38189600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr13:38189400-38189800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:38189400-38189800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:38189400-38189800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:38189400-38189800	Enhancers	HMEC	breast
11	chr13:38189400-38190400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:38189400-38191600	Enhancers	HSMM	muscle
13	chr13:38189400-38191600	Enhancers	Osteobl	bone
14	chr13:38189400-38192800	Enhancers	NH-A	brain

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