Variant report

Variant	rs2413980
Chromosome Location	chr15:50221358-50221359
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50218645..50222187-chr15:50222298..50224659,3	MCF-7	breast:
2	chr15:50217382..50219083-chr15:50219273..50221734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10519249	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[ASN][1000 genomes]
rs11070737	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11070738	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs11070740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853540	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs12437526	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12438914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439937	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440802	0.89[ASN][1000 genomes]
rs12442429	0.91[CEU][hapmap]
rs12442430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs12442475	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12442538	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs12442825	0.89[ASN][1000 genomes]
rs12443320	0.90[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs12903572	0.90[ASN][1000 genomes]
rs12909968	0.89[ASN][1000 genomes]
rs16963149	0.85[CHD][hapmap]
rs16963151	0.82[CHD][hapmap]
rs2413981	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2413982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413987	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs2413989	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2413993	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs2413994	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2452524	0.81[ASN][1000 genomes]
rs2899443	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899444	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34032545	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35434426	0.89[ASN][1000 genomes]
rs35453457	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4143620	0.90[CHB][hapmap]
rs4238378	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4387547	0.89[ASN][1000 genomes]
rs4471619	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4497628	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60343610	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493392	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[ASN][1000 genomes]
rs7164800	0.84[ASN][1000 genomes]
rs7166047	0.91[CEU][hapmap]
rs7173644	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs7174815	0.81[ASN][1000 genomes]
rs7176332	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72623973	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8027678	0.85[CHD][hapmap]
rs8029355	0.82[CEU][hapmap]
rs8034382	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs8039142	0.88[CHD][hapmap]
rs8041517	1.00[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2413980	C15orf63	cis	parietal	SCAN
rs2413980	FGF7	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50205400-50234400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:50210200-50232400	Strong transcription	Primary hematopoietic stem cells	blood
3	chr15:50210800-50226400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:50211000-50227200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:50211400-50232400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:50217600-50226400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:50218000-50224000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:50218600-50227200	Weak transcription	Liver	Liver
9	chr15:50219800-50222800	Weak transcription	Placenta	Placenta
10	chr15:50219800-50223800	Weak transcription	Brain Substantia Nigra	brain
11	chr15:50220600-50226000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:50220800-50226400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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