Variant report

Variant	rs6904723
Chromosome Location	chr6:38436317-38436318
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38435448..38438389-chr6:38439030..38441795,2	MCF-7	breast:
2	chr6:38423292..38425801-chr6:38436010..38438215,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12191714	1.00[JPT][hapmap]
rs12206324	1.00[JPT][hapmap]
rs12206905	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12212983	1.00[JPT][hapmap]
rs12215850	1.00[JPT][hapmap]
rs1883610	0.86[JPT][hapmap]
rs1983605	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28445226	1.00[JPT][hapmap]
rs4236058	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4711542	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4711546	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4714148	0.88[CHD][hapmap]
rs4714152	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4714157	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714161	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714164	0.85[ASN][1000 genomes]
rs4714165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60936387	0.86[ASN][1000 genomes]
rs61192259	0.86[ASN][1000 genomes]
rs6458054	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909898	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6933268	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6933758	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6940319	1.00[JPT][hapmap]
rs742515	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7748599	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7749685	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7759629	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7766214	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7770868	0.88[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs871183	1.00[JPT][hapmap]
rs9349073	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9357272	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9380743	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9394492	0.88[CHD][hapmap]
rs9394495	1.00[JPT][hapmap]
rs9394500	0.85[ASN][1000 genomes]
rs9470885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470888	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9470891	0.88[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6904723	GLO1	cis	parietal	SCAN
rs6904723	GLO1	cis	cerebellum	SCAN
rs6904723	BYSL	cis	parietal	SCAN
rs6904723	MDGA1	cis	cerebellum	SCAN
rs6904723	C6orf106	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:38412200-38445600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:38414000-38438400	Weak transcription	Left Ventricle	heart
4	chr6:38425200-38438400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:38427600-38437200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:38436200-38437000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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