Variant report

Variant	rs1456104
Chromosome Location	chr3:157126631-157126632
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	chr3:157120587..157122902-chr3:157126079..157127970,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1014855	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074864	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10755111	0.85[JPT][hapmap]
rs10936077	0.81[JPT][hapmap]
rs10936088	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10936089	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392798	0.87[MEX][hapmap]
rs1403105	0.85[JPT][hapmap]
rs1456109	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2316712	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321743	0.85[JPT][hapmap]
rs3911402	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679790	0.85[JPT][hapmap]
rs4679791	0.85[JPT][hapmap]
rs4680353	0.85[JPT][hapmap]
rs722485	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9831686	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9837655	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9848774	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3397270	chr3:157126467-157126719	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1456104	C3orf55	cis	parietal	SCAN
rs1456104	SSR3	cis	cerebellum	SCAN
rs1456104	PTX3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
2	chr3:157107400-157128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:157113400-157129800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:157116000-157128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:157119000-157142800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:157120000-157142600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:157120200-157135800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:157123000-157135000	Weak transcription	Spleen	Spleen
9	chr3:157123600-157129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:157123800-157128600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:157123800-157130000	Weak transcription	NH-A	brain
12	chr3:157124400-157131200	Weak transcription	Osteobl	bone
13	chr3:157124400-157134200	Weak transcription	HSMM	muscle
14	chr3:157124400-157135800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:157124600-157129600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:157124600-157134800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:157125800-157129400	Weak transcription	HUVEC	blood vessel
18	chr3:157126400-157126800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:157126400-157127200	Enhancers	NHEK	skin
20	chr3:157126400-157127400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:157126600-157127000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:157126600-157135400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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