Variant report

Variant	rs1138873
Chromosome Location	chr8:104279038-104279039
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	chr8:104268461..104270689-chr8:104277441..104279218,2	MCF-7	breast:
2	chr8:104156664..104158879-chr8:104277049..104279566,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8orf56-1	chr8:104278773-104279748	NONHSAT128175
2	lnc-C8orf56-1	chr8:104278875-104279719	NONHSAT128169

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12541167	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12543038	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13275377	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13278361	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13278540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1353212	0.95[CHB][hapmap];0.87[AMR][1000 genomes]
rs1353213	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs1403293	0.86[AMR][1000 genomes]
rs1494278	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1522707	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16870243	0.84[AMR][1000 genomes]
rs16870245	0.84[AMR][1000 genomes]
rs16870249	0.84[AMR][1000 genomes]
rs17205332	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17799604	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1982892	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1982893	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2220825	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs3104031	0.86[AMR][1000 genomes]
rs3104033	0.86[JPT][hapmap]
rs3107646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3116457	0.89[AMR][1000 genomes]
rs3133824	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3133833	0.86[JPT][hapmap]
rs3133837	0.86[JPT][hapmap]
rs34185273	0.87[AMR][1000 genomes]
rs34201011	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34273148	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34337822	0.84[AMR][1000 genomes]
rs4734693	0.81[ASN][1000 genomes]
rs4734695	0.91[ASN][1000 genomes]
rs7002269	0.95[CHB][hapmap]
rs9656787	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[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	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1017326	chr8:104236193-104313235	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1138873	FZD6	cis	cerebellum	SCAN
rs1138873	SLC25A32	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104268200-104283400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:104268800-104281200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:104269000-104283400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:104269800-104283200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:104269800-104283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:104276000-104279400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:104276400-104279800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr8:104276600-104280200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:104276800-104280600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:104277000-104279400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:104277400-104279200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr8:104277400-104279600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr8:104277400-104279600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr8:104277800-104280600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:104278000-104279200	Weak transcription	NHDF-Ad	bronchial
16	chr8:104278200-104279400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:104278400-104279400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr8:104278400-104279800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:104279000-104279200	Enhancers	Fetal Stomach	stomach
20	chr8:104279000-104280000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr8:104279000-104280000	Strong transcription	Aorta	Aorta
22	chr8:104279000-104280800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr8:104279000-104281000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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