Variant report

Variant	rs6475551
Chromosome Location	chr9:21701639-21701640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10757236	0.82[ASN][1000 genomes]
rs10811584	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811592	0.82[ASN][1000 genomes]
rs10811595	0.82[ASN][1000 genomes]
rs12380505	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1335498	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335499	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335500	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335501	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335505	0.90[JPT][hapmap]
rs1372057	0.90[JPT][hapmap]
rs1372058	0.90[JPT][hapmap]
rs1372059	0.90[JPT][hapmap]
rs1414232	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414233	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414234	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414242	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1414244	0.90[JPT][hapmap]
rs1452658	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840050	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889680	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1965153	0.80[ASN][1000 genomes]
rs2004627	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2043991	0.82[ASN][1000 genomes]
rs2123338	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs2165411	0.82[ASN][1000 genomes]
rs2383202	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2891159	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2891164	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2891165	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35875883	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3928894	0.81[JPT][hapmap]
rs4352937	0.90[JPT][hapmap]
rs4548267	0.90[JPT][hapmap]
rs4560881	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4620363	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4636294	0.81[JPT][hapmap]
rs6475549	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475554	0.82[ASN][1000 genomes]
rs6475555	0.82[ASN][1000 genomes]
rs6475564	0.82[ASN][1000 genomes]
rs6475585	0.82[JPT][hapmap]
rs7023299	0.82[ASN][1000 genomes]
rs7023474	0.81[JPT][hapmap]
rs7028913	0.82[ASN][1000 genomes]
rs7029040	0.82[ASN][1000 genomes]
rs7029166	0.82[ASN][1000 genomes]
rs7029274	0.82[ASN][1000 genomes]
rs7039487	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7043827	0.82[ASN][1000 genomes]
rs7047136	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751173	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7848524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7854222	0.80[ASN][1000 genomes]
rs7855242	0.82[ASN][1000 genomes]
rs7857636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858959	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860576	0.82[ASN][1000 genomes]
rs7867994	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7868091	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7871345	0.82[ASN][1000 genomes]
rs9298821	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298822	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298823	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv892742	chr9:21589041-21707372	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv471290	chr9:21694038-21721939	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv892744	chr9:21694039-21746419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1837210	chr9:21700795-21729895	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6475551	MTAP	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21696600-21707000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:21699600-21707600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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