Variant report

Variant	rs12089739
Chromosome Location	chr1:98403034-98403035
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	chr1:98385061..98387939-chr1:98401508..98404733,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188641	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11165915	1.00[AMR][1000 genomes]
rs11165919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11165925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11165927	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11165929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11165931	1.00[AMR][1000 genomes]
rs11165932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11165933	1.00[AMR][1000 genomes]
rs11165942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12065481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12066038	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12067602	0.83[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12071573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071668	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12076723	1.00[AMR][1000 genomes]
rs12078010	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12078571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080892	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12087574	1.00[AMR][1000 genomes]
rs12087601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091195	1.00[AMR][1000 genomes]
rs12092358	1.00[AMR][1000 genomes]
rs12093406	1.00[AMR][1000 genomes]
rs12093707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097552	1.00[AMR][1000 genomes]
rs28703292	1.00[AMR][1000 genomes]
rs74106027	1.00[AMR][1000 genomes]
rs74106028	1.00[AMR][1000 genomes]
rs74106030	1.00[AMR][1000 genomes]
rs74106031	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98400400-98407000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:98401400-98404000	Enhancers	Brain Cingulate Gyrus	brain
3	chr1:98401600-98406400	Weak transcription	Dnd41	blood
4	chr1:98402000-98404000	Enhancers	Brain Substantia Nigra	brain
5	chr1:98402000-98404800	Enhancers	HMEC	breast
6	chr1:98402200-98403800	Enhancers	Brain Anterior Caudate	brain
7	chr1:98402200-98404000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:98402200-98404000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr1:98402400-98403400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:98402400-98404400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:98402400-98404600	Enhancers	NHEK	skin
12	chr1:98402400-98404800	Enhancers	Hela-S3	cervix
13	chr1:98402600-98403200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:98402600-98403400	Enhancers	A549	lung
15	chr1:98402600-98403400	Enhancers	NH-A	brain
16	chr1:98402600-98403800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:98402600-98403800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:98402600-98403800	Enhancers	HSMM	muscle
19	chr1:98402600-98403800	Enhancers	NHDF-Ad	bronchial
20	chr1:98402600-98404200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:98402600-98404200	Enhancers	NHLF	lung
22	chr1:98402600-98404600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:98402600-98404600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:98402600-98404600	Enhancers	HUVEC	blood vessel
25	chr1:98402800-98403800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:98402800-98403800	Weak transcription	Placenta	Placenta
27	chr1:98402800-98403800	Enhancers	Osteobl	bone
28	chr1:98402800-98404200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:98402800-98404200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:98402800-98404200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:98402800-98407800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:98403000-98403800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr1:98403000-98404200	Enhancers	HSMMtube	muscle
34	chr1:98403000-98404600	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links