Variant report

Variant	rs10246308
Chromosome Location	chr7:41301819-41301820
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10214988	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10214990	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10215332	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10215556	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10215561	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10215670	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10225564	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10225707	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10230756	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10238779	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10242681	0.85[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10258437	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281338	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10951648	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11505532	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11505535	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11760865	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11765437	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11766101	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11768187	0.86[ASN][1000 genomes]
rs11972895	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11976671	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12154794	0.86[ASN][1000 genomes]
rs12155345	0.86[ASN][1000 genomes]
rs12155372	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12674340	0.90[EUR][1000 genomes]
rs12701875	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12701876	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12701877	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12701879	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12701880	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12701882	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230373	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13238496	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1545195	0.86[ASN][1000 genomes]
rs1557929	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1557931	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158558	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2189841	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35796717	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6944817	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6948410	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6955172	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6966153	0.85[ASN][1000 genomes]
rs6974692	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs718224	0.86[ASN][1000 genomes]
rs7796964	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs985821	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv534465	chr7:41224437-41443498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10246308	NPC1L1	cis	parietal	SCAN
rs10246308	C7orf10	cis	parietal	SCAN
rs10246308	MYL7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41296800-41343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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