Variant report

No.	Distal block	Cell Line	Cell type
1	chr9:116065580..116067565-chr9:116101050..116102835,2	MCF-7	breast:
2	chr9:116036612..116039217-chr9:116063138..116067985,4	MCF-7	breast:
3	chr9:116063473..116067468-chr9:116171615..116174364,4	MCF-7	breast:
4	chr9:116065546..116067131-chr9:116136857..116139618,2	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10124515	0.85[CHB][hapmap]
rs10817475	0.80[CHB][hapmap]
rs10981713	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs10981714	0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10981718	0.88[ASN][1000 genomes]
rs10981719	0.90[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10981734	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs12378096	0.95[LWK][hapmap]
rs16932730	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2093691	0.82[CHB][hapmap]
rs2296075	0.85[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2418249	0.85[CHB][hapmap]
rs4979232	0.80[CHB][hapmap]
rs59841233	0.93[ASN][1000 genomes]
rs6478001	0.83[ASN][1000 genomes]
rs7038589	0.95[LWK][hapmap]
rs71503561	0.95[ASN][1000 genomes]
rs7849513	0.81[CHB][hapmap]
rs7860625	0.81[CHB][hapmap]
rs7868271	0.82[CHB][hapmap]
rs7873862	0.81[CHB][hapmap]
rs912247	0.87[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10817476	SLC31A1	Cis_1M	lymphoblastoid	RTeQTL
rs10817476	SLC31A1	cis	parietal	SCAN
rs10817476	BSPRY	cis	parietal	SCAN
rs10817476	ZNF618	cis	parietal	SCAN
rs10817476	EPB41L4B	cis	cerebellum	SCAN
rs10817476	WDR31	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116062600-116075600	Weak transcription	Placenta	Placenta
4	chr9:116065400-116086800	Weak transcription	Gastric	stomach
5	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
7	chr9:116065800-116069800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:116066000-116069800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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