Variant report

Variant	rs12488821
Chromosome Location	chr3:22002998-22002999
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	chr11:126141332..126144254-chr3:22001697..22003217,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBE2E2-2	chr3:22002908-22003032	ENSG00000223351

Variant related genes	Relation type
ENSG00000110074	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11129035	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129036	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487974	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489570	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631100	0.84[ASN][1000 genomes]
rs12634207	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634535	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636900	0.93[ASN][1000 genomes]
rs12638192	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639321	0.93[ASN][1000 genomes]
rs1383075	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1479960	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs166317	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17644025	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17644255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2291817	0.91[ASN][1000 genomes]
rs2291818	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291819	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291820	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336520	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34995962	0.84[ASN][1000 genomes]
rs3821391	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559467	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs563129	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58842146	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66530626	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67125873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763267	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6765798	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68055552	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72625849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72625850	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7619247	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642008	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2751992	chr3:21786893-22212357	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv948555	chr3:21786893-22212357	Active TSS Enhancers Flanking Active TSS Weak transcription 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
4	nsv1003085	chr3:21887971-22415107	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv834633	chr3:21918264-22088338	Enhancers Weak transcription 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	nsv876616	chr3:21946847-22310622	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv876617	chr3:21955784-22310622	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv999478	chr3:21971861-22012241	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv1000732	chr3:21976969-22012241	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv1007663	chr3:21984364-22022923	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	nsv1014467	chr3:21985380-22008097	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	nsv1014852	chr3:21985380-22010086	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	nsv1012249	chr3:21985380-22012241	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
14	nsv1009404	chr3:21985380-22018041	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	nsv1001030	chr3:21985380-22022923	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv460474	chr3:21985417-22047934	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
17	nsv589932	chr3:21985417-22047934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv1007886	chr3:21985691-22018041	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv998319	chr3:21999480-22033364	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
20	nsv432404	chr3:22000296-22433396	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21997400-22003000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:21997600-22003200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:22001600-22003600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:22002200-22003600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links