Variant report

Variant	rs2959003
Chromosome Location	chr15:74628891-74628892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74622577..74624588-chr15:74627714..74630586,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11072478	0.80[CEU][hapmap]
rs12440952	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs12916123	0.88[CEU][hapmap]
rs12916765	0.92[EUR][1000 genomes]
rs1564782	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1564783	0.81[EUR][1000 genomes]
rs1843090	0.88[CEU][hapmap]
rs1843091	0.87[CEU][hapmap]
rs2277601	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2277602	0.92[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs2277605	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2277606	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2279356	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2279357	0.88[CEU][hapmap]
rs2930300	0.80[CEU][hapmap]
rs2930302	0.80[CEU][hapmap]
rs2930304	0.92[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs2930306	0.88[CEU][hapmap]
rs2959002	0.80[AMR][1000 genomes]
rs2959004	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2959006	0.80[CEU][hapmap]
rs2959007	0.80[CEU][hapmap]
rs2959008	0.80[CEU][hapmap]
rs2959011	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs4077581	0.92[CEU][hapmap]
rs4077582	0.92[CEU][hapmap]
rs6495096	0.88[CEU][hapmap]
rs7173655	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174179	0.88[CEU][hapmap]
rs751527	0.85[EUR][1000 genomes]
rs8031121	0.92[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs8031424	0.91[CEU][hapmap]
rs8039847	0.86[EUR][1000 genomes]
rs900798	0.97[EUR][1000 genomes]
rs900802	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2959003	C15orf39	cis	cerebellum	SCAN
rs2959003	RPLP1	cis	parietal	SCAN
rs2959003	SLC2A3	trans	brain	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74612000-74657800	Weak transcription	Right Atrium	heart
2	chr15:74622600-74638600	Weak transcription	Spleen	Spleen
3	chr15:74627400-74631800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:74628000-74642200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:74628200-74629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:74628400-74630800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:74628400-74632200	Genic enhancers	Placenta	Placenta
8	chr15:74628600-74629800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr15:74628600-74629800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:74628600-74630000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:74628600-74632000	Enhancers	Hela-S3	cervix
12	chr15:74628800-74629000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr15:74628800-74629400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:74628800-74629400	Enhancers	Osteobl	bone
15	chr15:74628800-74629800	Enhancers	NHDF-Ad	bronchial

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