Variant report

Variant	rs2409730
Chromosome Location	chr8:11060638-11060639
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTMR9-3	chr8:11058877-11061136	NONHSAT125041
2	lnc-MTMR9-3	chr8:11060474-11061180	ENSG00000270076.1

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10100660	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10108967	0.89[ASN][1000 genomes]
rs10110684	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10503415	1.00[CHB][hapmap]
rs11250119	1.00[CHB][hapmap]
rs11775489	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11777355	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11777887	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11777918	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11783045	0.84[ASW][hapmap];0.91[CEU][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11783890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11989369	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13265553	0.81[TSI][hapmap]
rs1987190	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2409719	0.81[TSI][hapmap]
rs2409720	0.93[ASW][hapmap];0.91[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2409725	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2409726	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2409727	0.81[AMR][1000 genomes]
rs2409729	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3021495	0.81[TSI][hapmap]
rs35223712	0.81[AMR][1000 genomes]
rs4412337	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4451268	0.85[ASW][hapmap];0.95[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4841504	1.00[CHB][hapmap]
rs4841507	0.81[TSI][hapmap]
rs59304760	0.89[ASN][1000 genomes]
rs59340759	0.89[ASN][1000 genomes]
rs73530579	0.89[ASN][1000 genomes]
rs9329238	0.85[ASW][hapmap];0.95[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2409730	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2409730	MTMR9	cis	parietal	SCAN
rs2409730	TDH	cis	cerebellum	SCAN
rs2409730	MFHAS1	cis	cerebellum	SCAN
rs2409730	FLJ10661	cis	cerebellum	SCAN
rs2409730	TDH	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11059800-11061800	Weak transcription	HSMMtube	muscle
2	chr8:11059800-11067400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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