Variant report

Variant	rs17049234
Chromosome Location	chr2:58111521-58111522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58110610..58113165-chr2:58114758..58117259,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12104766	1.00[AMR][1000 genomes]
rs12105180	1.00[AMR][1000 genomes]
rs1520963	1.00[AMR][1000 genomes]
rs17039675	1.00[AMR][1000 genomes]
rs17049103	1.00[AMR][1000 genomes]
rs17049119	1.00[AMR][1000 genomes]
rs17049122	1.00[AMR][1000 genomes]
rs17049169	1.00[AMR][1000 genomes]
rs17049188	1.00[AMR][1000 genomes]
rs17049192	1.00[AMR][1000 genomes]
rs17049195	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049213	0.82[AFR][1000 genomes]
rs17049218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049246	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049251	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs41507950	1.00[AMR][1000 genomes]
rs55811651	1.00[AMR][1000 genomes]
rs56193241	1.00[AMR][1000 genomes]
rs56199322	1.00[AMR][1000 genomes]
rs56393555	1.00[AMR][1000 genomes]
rs58333652	1.00[AMR][1000 genomes]
rs58838819	1.00[AMR][1000 genomes]
rs59146679	1.00[AMR][1000 genomes]
rs59163667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59235511	1.00[AMR][1000 genomes]
rs59691581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60453955	1.00[AMR][1000 genomes]
rs60462720	1.00[AMR][1000 genomes]
rs60765249	1.00[AMR][1000 genomes]
rs6751864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72939601	1.00[AMR][1000 genomes]
rs72941503	1.00[AMR][1000 genomes]
rs72941525	1.00[AMR][1000 genomes]
rs72941526	1.00[AMR][1000 genomes]
rs72941532	1.00[AMR][1000 genomes]
rs72941544	1.00[AMR][1000 genomes]
rs72941589	1.00[AMR][1000 genomes]
rs72943305	1.00[AMR][1000 genomes]
rs72943312	1.00[AMR][1000 genomes]
rs72943328	1.00[AMR][1000 genomes]
rs72943335	1.00[AMR][1000 genomes]
rs72943342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943356	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943358	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943369	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943371	1.00[AMR][1000 genomes]
rs73941649	1.00[AMR][1000 genomes]
rs73942209	1.00[AMR][1000 genomes]
rs73942219	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73942274	1.00[AMR][1000 genomes]
rs73942288	1.00[AMR][1000 genomes]
rs73944124	1.00[AMR][1000 genomes]
rs73944146	1.00[AMR][1000 genomes]
rs7572606	0.90[LWK][hapmap];1.00[AMR][1000 genomes]
rs7600283	1.00[AMR][1000 genomes]
rs952625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs952626	1.00[AFR][1000 genomes];1.00[AMR][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	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834148	chr2:57979661-58119213	Weak transcription Enhancers Flanking Active TSS Active 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	2 gene(s)	inside rSNPs	diseases
4	nsv1010981	chr2:58013389-58205699	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv874199	chr2:58031249-58161520	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58106000-58113000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:58106000-58113400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:58106000-58113400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:58106000-58113400	Weak transcription	Pancreas	Pancrea
5	chr2:58106400-58113600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:58108600-58111600	Weak transcription	Fetal Brain Female	brain
7	chr2:58110000-58113400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:58110400-58112200	Weak transcription	Fetal Brain Male	brain
9	chr2:58110400-58112800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:58110400-58113200	Weak transcription	Osteobl	bone
11	chr2:58110400-58117200	Weak transcription	NHDF-Ad	bronchial
12	chr2:58110600-58111600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:58110600-58111600	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:58110600-58112200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:58110600-58112400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:58110600-58112400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:58110600-58112600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:58110600-58112600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:58110600-58112800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:58110600-58112800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:58110600-58113000	Weak transcription	Brain Anterior Caudate	brain
22	chr2:58110600-58117400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:58110600-58117400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:58110800-58113800	Enhancers	A549	lung
25	chr2:58111400-58111600	Enhancers	Hela-S3	cervix
26	chr2:58111400-58111800	Flanking Active TSS	GM12878-XiMat	blood
27	chr2:58111400-58112800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links