Variant report

Variant	rs3112130
Chromosome Location	chr12:24693304-24693305
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:24687694..24690051-chr12:24691689..24693525,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10743510	1.00[EUR][1000 genomes]
rs10771101	1.00[EUR][1000 genomes]
rs10771102	1.00[EUR][1000 genomes]
rs1115525	1.00[EUR][1000 genomes]
rs1386640	1.00[AMR][1000 genomes]
rs1386641	1.00[EUR][1000 genomes]
rs1386642	1.00[AMR][1000 genomes]
rs1386643	1.00[EUR][1000 genomes]
rs1487652	1.00[EUR][1000 genomes]
rs1487659	1.00[AMR][1000 genomes]
rs1811606	1.00[AMR][1000 genomes]
rs2354628	1.00[EUR][1000 genomes]
rs2955480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2955482	1.00[EUR][1000 genomes]
rs2955483	1.00[EUR][1000 genomes]
rs2955488	1.00[AMR][1000 genomes]
rs2955489	1.00[AMR][1000 genomes]
rs2970414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2970421	1.00[AMR][1000 genomes]
rs3110019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3110020	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3112131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4029339	1.00[EUR][1000 genomes]
rs4348994	1.00[EUR][1000 genomes]
rs4963576	1.00[AMR][1000 genomes]
rs4963578	1.00[AMR][1000 genomes]
rs4963585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6487392	1.00[AMR][1000 genomes]
rs6487402	1.00[EUR][1000 genomes]
rs7136885	1.00[EUR][1000 genomes]
rs7307756	1.00[AMR][1000 genomes]
rs7312721	1.00[AMR][1000 genomes]
rs936901	1.00[EUR][1000 genomes]
rs962728	1.00[EUR][1000 genomes]
rs997025	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv832352	chr12:24534823-24736540	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1046463	chr12:24538432-24916851	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv915555	chr12:24666481-24952013	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv645	chr12:24683914-24723421	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24688600-24693400	Weak transcription	Fetal Brain Male	brain
2	chr12:24688800-24693800	Weak transcription	Fetal Brain Female	brain
3	chr12:24689000-24693800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:24689200-24703800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:24689800-24693400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:24690000-24694200	Enhancers	Liver	Liver
7	chr12:24690600-24695000	Weak transcription	Small Intestine	intestine
8	chr12:24691000-24694000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:24691000-24696800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:24691200-24693600	Enhancers	Fetal Lung	lung
11	chr12:24691200-24693600	Weak transcription	Fetal Stomach	stomach
12	chr12:24691400-24693800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:24691400-24703600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:24691600-24695000	Weak transcription	Adipose Nuclei	Adipose
15	chr12:24691600-24695000	Weak transcription	Ovary	ovary
16	chr12:24691600-24699400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:24692200-24695200	Enhancers	NHLF	lung
18	chr12:24692800-24694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:24692800-24694600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:24693000-24693400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:24693000-24693400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr12:24693000-24694000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links