Variant report

Variant	rs13408524
Chromosome Location	chr2:31414223-31414224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31410117..31413014-chr2:31413496..31415542,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10180414	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10203856	0.83[ASN][1000 genomes]
rs10445909	0.85[ASN][1000 genomes]
rs12105593	0.85[ASN][1000 genomes]
rs12468547	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477841	0.83[ASN][1000 genomes]
rs12992405	0.82[CHB][hapmap]
rs13382984	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13387367	0.85[ASN][1000 genomes]
rs13387507	0.83[ASN][1000 genomes]
rs13389654	0.81[ASN][1000 genomes]
rs13389667	0.81[ASN][1000 genomes]
rs13409609	0.82[ASN][1000 genomes]
rs13421448	0.82[ASN][1000 genomes]
rs13421721	0.81[ASN][1000 genomes]
rs13423585	0.85[ASN][1000 genomes]
rs1348437	0.92[CHB][hapmap]
rs1443706	0.83[ASN][1000 genomes]
rs1443707	0.83[ASN][1000 genomes]
rs1443708	0.92[CHB][hapmap]
rs1465972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465973	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465974	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465975	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465976	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1562021	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17010910	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2028676	0.83[ASN][1000 genomes]
rs2028677	0.81[ASN][1000 genomes]
rs2028678	0.83[ASN][1000 genomes]
rs2044245	1.00[CHB][hapmap]
rs2044246	0.92[CHB][hapmap]
rs28376508	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4245767	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4516476	0.82[ASN][1000 genomes]
rs4592896	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs4951968	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952051	0.92[CHB][hapmap]
rs4952053	0.83[ASN][1000 genomes]
rs4952054	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55741080	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55817058	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56373046	0.85[ASN][1000 genomes]
rs57684646	0.81[ASN][1000 genomes]
rs57740838	0.85[ASN][1000 genomes]
rs59788807	0.85[ASN][1000 genomes]
rs60854003	0.83[ASN][1000 genomes]
rs61245117	0.83[ASN][1000 genomes]
rs6543611	0.81[ASN][1000 genomes]
rs6715931	0.81[ASN][1000 genomes]
rs6720254	0.81[ASN][1000 genomes]
rs6741329	0.92[CHB][hapmap]
rs72797132	0.85[ASN][1000 genomes]
rs734281	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7422120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556787	0.81[ASN][1000 genomes]
rs7564370	0.83[ASN][1000 genomes]
rs7564478	0.81[ASN][1000 genomes]
rs7570373	0.81[ASN][1000 genomes]
rs7578398	0.83[ASN][1000 genomes]
rs7595928	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764072	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9308916	1.00[CHB][hapmap]
rs9308917	0.91[CHB][hapmap]
rs961641	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs961642	0.92[CHB][hapmap]
rs9753207	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873771	chr2:31363732-31416582	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873772	chr2:31363732-31417863	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873773	chr2:31363732-31426449	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv873774	chr2:31363732-31432367	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873776	chr2:31384009-31439443	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv997652	chr2:31385242-31431588	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv535611	chr2:31385242-31431588	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13408524	Hs.468081	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31391200-31418600	Weak transcription	Gastric	stomach
2	chr2:31394800-31419600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:31395200-31416600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:31395800-31415000	Weak transcription	Esophagus	oesophagus
5	chr2:31404000-31415800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:31410400-31414600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:31410800-31420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:31411000-31421800	Weak transcription	Primary T cells from cord blood	blood
9	chr2:31411000-31427400	Weak transcription	Fetal Brain Female	brain
10	chr2:31411200-31436800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:31412800-31416800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:31413200-31417400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:31413400-31425600	Weak transcription	Right Ventricle	heart
14	chr2:31413800-31416200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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