Variant report

Variant	rs13394720
Chromosome Location	chr2:234502121-234502122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:234498935-234505513..2:234666975-234672018	Hela-S3	cervix:
2	2:234498935-234505513..2:234835115-234838817	Hela-S3	cervix:
3	2:234498935-234505513..2:234683624-234705119	K562	blood:
4	2:234498935-234505513..2:234635414-234639782	Hela-S3	cervix:
5	2:234498935-234505513..2:234898811-234918017	Hela-S3	cervix:
6	2:234498935-234505513..2:234572898-234594986	K562	blood:
7	2:234498935-234505513..2:234825998-234827518	Hela-S3	cervix:
8	2:234498935-234505513..2:234543708-234558325	H1-hESC	embryonic stem cell:	embryo
9	2:234498935-234505513..2:234743181-234749667	Hela-S3	cervix:
10	2:234498935-234505513..2:234954947-234965240	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000185038	Chromatin interaction
ENSG00000244122	Chromatin interaction
ENSG00000242515	Chromatin interaction
ENSG00000072080	Chromatin interaction
ENSG00000241119	Chromatin interaction
ENSG00000241635	Chromatin interaction
ENSG00000144481	Chromatin interaction
ENSG00000234143	Chromatin interaction
ENSG00000242366	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000243135	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10176427	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10182651	0.96[EUR][1000 genomes]
rs1042590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13383300	0.96[EUR][1000 genomes]
rs13383893	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13385018	0.83[GIH][hapmap]
rs13387539	0.96[EUR][1000 genomes]
rs13390446	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13394291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13395023	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13401136	0.87[EUR][1000 genomes]
rs13405703	0.83[EUR][1000 genomes]
rs13408490	0.83[EUR][1000 genomes]
rs13417719	0.96[EUR][1000 genomes]
rs13430633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13432903	0.87[EUR][1000 genomes]
rs17864662	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17868296	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28946875	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4132954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55773422	0.82[ASN][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv3445986	chr2:234494952-234557707	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	nsv876014	chr2:234495742-234545861	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
6	esv3419326	chr2:234498411-234560470	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 control	20041166	GWAS catalog

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234500600-234502200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:234501600-234502200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:234501600-234502200	Flanking Active TSS	GM12878-XiMat	blood
4	chr2:234501600-234502600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:234502000-234502600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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