Variant report

Variant	rs3104033
Chromosome Location	chr8:104278419-104278420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104277174..104278799-chr8:104425845..104427613,2	MCF-7	breast:
2	chr8:104268461..104270689-chr8:104277441..104279218,2	MCF-7	breast:
3	chr8:104156664..104158879-chr8:104277049..104279566,2	MCF-7	breast:
4	chr8:104259482..104261935-chr8:104276348..104278558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164934	Chromatin interaction
ENSG00000164933	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];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1053917	0.85[GIH][hapmap]
rs1095713	0.84[GIH][hapmap]
rs1157213	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs12541167	0.81[JPT][hapmap]
rs12543038	0.81[JPT][hapmap]
rs13277869	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs1494280	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1522712	0.81[CEU][hapmap]
rs17205332	0.81[CHB][hapmap]
rs2220824	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2934726	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3133798	0.96[CEU][hapmap];0.95[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3133837	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]
rs3808553	0.87[GIH][hapmap]
rs3808554	0.87[GIH][hapmap]
rs6999018	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001084	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs7825986	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7829782	0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs827535	0.84[GIH][hapmap]
rs827536	0.84[GIH][hapmap]
rs827541	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[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
rs3104033	C8orf56	cis	cerebellum	SCAN
rs3104033	SLC25A32	cis	cerebellum	SCAN
rs3104033	GRHL2	cis	cerebellum	SCAN
rs3104033	FZD6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104252200-104279000	Weak transcription	Aorta	Aorta
2	chr8:104268200-104283400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:104268800-104281200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr8:104269000-104283400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:104269800-104283200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:104269800-104283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:104276000-104279400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:104276400-104279800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr8:104276600-104279000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:104276600-104280200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:104276800-104280600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:104277000-104279400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr8:104277400-104279000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr8:104277400-104279200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr8:104277400-104279600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr8:104277400-104279600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr8:104277600-104279000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr8:104277800-104280600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr8:104278000-104279000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr8:104278000-104279200	Weak transcription	NHDF-Ad	bronchial
21	chr8:104278200-104279400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:104278400-104279400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr8:104278400-104279800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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