Variant report

Variant	rs3133837
Chromosome Location	chr8:104280769-104280770
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	chr8:104279333..104281935-chr8:104310595..104312938,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164930	Chromatin interaction
ENSG00000247081	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10096928	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1053917	0.85[GIH][hapmap]
rs1095713	0.81[CHD][hapmap];0.84[GIH][hapmap]
rs1157213	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs12541167	0.81[JPT][hapmap]
rs12543038	0.81[JPT][hapmap]
rs13277869	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs1494280	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1522712	0.81[CEU][hapmap]
rs17205332	0.81[CHB][hapmap]
rs2220824	1.00[CHB][hapmap]
rs2934726	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3104033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133798	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3133833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808553	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs3808554	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs6999018	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7001084	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs7825986	1.00[CHB][hapmap]
rs7829782	0.94[CHB][hapmap];0.87[CHD][hapmap]
rs827535	0.84[GIH][hapmap]
rs827536	0.84[GIH][hapmap]
rs827541	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827581	0.82[GIH][hapmap]
rs827584	0.85[GIH][hapmap]
rs827585	0.85[GIH][hapmap]
rs827588	0.82[GIH][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3133837	C8orf56	cis	cerebellum	SCAN
rs3133837	FZD6	cis	cerebellum	SCAN
rs3133837	SLC25A32	cis	cerebellum	SCAN
rs3133837	GRHL2	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr8:104279000-104280800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:104279000-104281000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr8:104279200-104282600	Enhancers	NHDF-Ad	bronchial
9	chr8:104279400-104282000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:104279400-104282400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:104279400-104282600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:104279400-104282800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:104279600-104281200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:104279600-104282600	Enhancers	Osteobl	bone
15	chr8:104279600-104282800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr8:104279600-104282800	Enhancers	NHLF	lung
17	chr8:104279800-104281200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr8:104279800-104281800	Enhancers	HSMM	muscle
19	chr8:104280000-104283400	Weak transcription	Aorta	Aorta
20	chr8:104280200-104283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:104280400-104281000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr8:104280600-104280800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:104280600-104281200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:104280600-104281800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:104280600-104281800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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