Variant report

Variant	rs12620592
Chromosome Location	chr2:78945592-78945593
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11126682	0.88[EUR][1000 genomes]
rs11676099	0.92[EUR][1000 genomes]
rs11690283	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11886800	0.91[EUR][1000 genomes]
rs11902387	0.92[EUR][1000 genomes]
rs11902428	0.91[EUR][1000 genomes]
rs12620510	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622478	0.85[EUR][1000 genomes]
rs1452044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015607	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17015611	0.89[EUR][1000 genomes]
rs17015634	0.88[EUR][1000 genomes]
rs1879112	0.83[ASN][1000 genomes]
rs2167558	0.88[EUR][1000 genomes]
rs57943624	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58039460	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59174671	0.80[ASN][1000 genomes]
rs59504369	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6720391	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6723382	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6737219	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6737473	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6739221	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6739558	0.92[EUR][1000 genomes]
rs6739900	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6754548	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72921874	0.88[EUR][1000 genomes]
rs72923747	0.83[EUR][1000 genomes]
rs73943159	0.81[ASN][1000 genomes]
rs73943257	0.88[EUR][1000 genomes]
rs73943258	0.88[EUR][1000 genomes]
rs73943259	0.86[EUR][1000 genomes]
rs73943260	0.85[EUR][1000 genomes]
rs73943261	0.82[EUR][1000 genomes]
rs7579066	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7605836	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3584761	chr2:78545020-79430628	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv998961	chr2:78574081-79150087	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv428052	chr2:78615333-79075603	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv874367	chr2:78658280-78945755	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv874370	chr2:78668935-79013457	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1002153	chr2:78841778-78945592	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv2755345	chr2:78857845-79045945	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv874373	chr2:78914837-79010908	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78944200-78945800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:78944600-78945800	Enhancers	Brain Germinal Matrix	brain
3	chr2:78944600-78946800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:78945000-78945600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr2:78945000-78946000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr2:78945200-78946200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:78945400-78945800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links