Variant report

Variant	rs12138538
Chromosome Location	chr1:153235837-153235838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11205254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126968	0.83[ASN][1000 genomes]
rs12131158	0.94[ASN][1000 genomes]
rs12137890	0.83[ASN][1000 genomes]
rs12138015	0.83[ASN][1000 genomes]
rs6661601	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6666892	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6672400	0.86[CHB][hapmap]
rs6690615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7518709	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7518712	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7528877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542150	0.94[ASN][1000 genomes]
rs7554266	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003014	chr1:153209833-153263691	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv535172	chr1:153209833-153263691	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv998032	chr1:153210770-153264131	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153234600-153236000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
2	chr1:153234600-153236000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
3	chr1:153234600-153236200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr1:153234800-153236000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:153234800-153236000	Flanking Active TSS	GM12878-XiMat	blood
6	chr1:153234800-153236200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:153235000-153236000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr1:153235000-153236000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:153235000-153236200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr1:153235200-153236000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:153235200-153236200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
12	chr1:153235600-153236000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:153235600-153236200	Bivalent Enhancer	Primary B cells from cord blood	blood
14	chr1:153235600-153236200	Bivalent Enhancer	Primary T cells from cord blood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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