Variant report

Variant	rs3107646
Chromosome Location	chr8:104285531-104285532
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	chr8:104285055..104288416-chr8:104382209..104384778,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164932	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1138873	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12541167	0.94[MEX][hapmap];0.89[AMR][1000 genomes]
rs12543038	0.85[GIH][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes]
rs13275377	0.89[AMR][1000 genomes]
rs13278361	0.89[AMR][1000 genomes]
rs13278540	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1353212	0.86[AMR][1000 genomes]
rs1353213	0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs1403293	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1494278	0.89[AMR][1000 genomes]
rs1522707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568641	0.81[AMR][1000 genomes]
rs16870243	0.82[AMR][1000 genomes]
rs16870245	0.82[AMR][1000 genomes]
rs16870249	0.82[AMR][1000 genomes]
rs17205332	0.83[CEU][hapmap];0.89[AMR][1000 genomes]
rs17799604	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1965482	0.86[CHB][hapmap]
rs1982892	0.89[AMR][1000 genomes]
rs1982893	0.89[AMR][1000 genomes]
rs2220825	0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs2270525	0.86[CHB][hapmap]
rs3104031	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3107648	0.86[CHB][hapmap]
rs3116457	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3116462	0.81[AMR][1000 genomes]
rs3116468	0.86[CHB][hapmap]
rs3133798	0.83[JPT][hapmap]
rs3133824	0.89[AMR][1000 genomes]
rs3133825	0.86[CHB][hapmap]
rs3133834	0.86[CHB][hapmap]
rs3133835	0.86[CHB][hapmap]
rs34185273	0.86[AMR][1000 genomes]
rs34201011	0.89[AMR][1000 genomes]
rs34273148	0.89[AMR][1000 genomes]
rs34337822	0.82[AMR][1000 genomes]
rs827541	0.83[JPT][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3107646	MAN2A1	trans	lymphoblastoid	seeQTL
rs3107646	SLC25A32	cis	cerebellum	SCAN
rs3107646	FZD6	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104284000-104289600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:104284400-104287000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:104284800-104289600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:104284800-104295400	Weak transcription	Aorta	Aorta

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