Variant report

Variant	rs12039260
Chromosome Location	chr1:153267337-153267338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10888549	0.88[ASN][1000 genomes]
rs11205261	0.93[ASN][1000 genomes]
rs11205265	0.89[ASN][1000 genomes]
rs11585177	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12028855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127371	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12723766	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2916238	0.93[ASN][1000 genomes]
rs3856024	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3886614	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4319268	0.85[ASN][1000 genomes]
rs6587735	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587736	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv999024	chr1:153255005-153325685	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153261400-153269400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:153264200-153268400	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:153265000-153267800	Enhancers	Primary B cells from cord blood	blood
4	chr1:153265200-153267800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:153265600-153267600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:153266000-153267400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:153266200-153269200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153266800-153267600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:153266800-153267800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:153266800-153267800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:153266800-153284400	Weak transcription	Esophagus	oesophagus

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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