Variant report

Variant	rs6519766
Chromosome Location	chr22:29269991-29269992
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	chr22:29269063..29271237-chr22:29276306..29278177,2	MCF-7	breast:
2	chr22:29269180..29273924-chr22:29276506..29281046,6	K562	blood:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1065497	0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12165962	0.83[ASW][hapmap];0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs1318025	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1318026	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132528	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132529	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132531	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132533	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132536	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132543	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs132548	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2015500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2064261	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2097461	0.89[JPT][hapmap]
rs2213645	0.95[JPT][hapmap]
rs2239815	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2239828	0.96[CEU][hapmap]
rs2269577	0.89[JPT][hapmap]
rs2347447	0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs3788409	0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs469990	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469991	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469992	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4822998	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs5752809	0.89[JPT][hapmap]
rs5752812	0.89[JPT][hapmap]
rs5752826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762784	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs5762788	0.89[JPT][hapmap];0.95[MEX][hapmap]
rs5762795	0.83[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs5762870	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762874	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762877	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762880	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762936	0.95[JPT][hapmap]
rs5997408	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5997412	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005881	0.83[ASW][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs6005915	0.95[JPT][hapmap];0.91[MEX][hapmap]
rs6005936	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7287806	0.89[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs7287918	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs763073	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs8136297	0.82[EUR][1000 genomes]
rs8137262	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8142067	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9620841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9625619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv3589	chr22:29265164-29288935	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6519766	MN1	cis	cerebellum	SCAN
rs6519766	GAL3ST1	cis	cerebellum	SCAN
rs6519766	ZNRF3	cis	parietal	SCAN
rs6519766	XBP1	cis	cerebellum	SCAN
rs6519766	XBP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29266200-29278400	Weak transcription	Fetal Intestine Small	intestine
2	chr22:29266400-29270800	Weak transcription	HepG2	liver
3	chr22:29269400-29270000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29269400-29270000	Active TSS	Brain Angular Gyrus	brain
5	chr22:29269400-29271400	Enhancers	HSMMtube	muscle
6	chr22:29269600-29271200	Enhancers	Fetal Muscle Leg	muscle

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