Variant report

Variant	rs10193072
Chromosome Location	chr2:48528035-48528036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXN2-2	chr2:48527999-48528357	NONHSAT070619

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10153773	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10174717	0.92[ASN][1000 genomes]
rs10180295	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10186237	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10199431	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs10208124	0.95[ASN][1000 genomes]
rs11676168	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs11682044	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs11685861	1.00[YRI][hapmap]
rs11690690	1.00[YRI][hapmap]
rs12616792	0.89[ASN][1000 genomes]
rs12713008	0.89[ASN][1000 genomes]
rs12713009	0.86[ASN][1000 genomes]
rs13383364	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13385535	0.92[ASN][1000 genomes]
rs13386751	0.93[ASN][1000 genomes]
rs13387171	0.96[ASN][1000 genomes]
rs13388291	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[ASN][1000 genomes]
rs13426834	0.93[ASN][1000 genomes]
rs13432998	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs2471405	0.87[ASN][1000 genomes]
rs28806843	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28841370	0.88[ASN][1000 genomes]
rs4290706	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4411759	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs4438532	0.80[CEU][hapmap]
rs4547573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[ASN][1000 genomes]
rs4606978	0.80[CEU][hapmap]
rs4641990	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56352447	0.92[ASN][1000 genomes]
rs57668696	0.87[ASN][1000 genomes]
rs58660534	0.88[ASN][1000 genomes]
rs59264464	0.90[ASN][1000 genomes]
rs59412192	0.90[ASN][1000 genomes]
rs59761994	0.88[ASN][1000 genomes]
rs60677957	0.93[ASN][1000 genomes]
rs62136987	0.89[ASN][1000 genomes]
rs62137001	0.88[ASN][1000 genomes]
rs62137002	0.88[ASN][1000 genomes]
rs62137003	0.88[ASN][1000 genomes]
rs62137005	0.88[ASN][1000 genomes]
rs62137006	0.88[ASN][1000 genomes]
rs62137007	0.88[ASN][1000 genomes]
rs62137008	0.86[ASN][1000 genomes]
rs62137009	0.86[ASN][1000 genomes]
rs62138801	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6545026	0.92[YRI][hapmap]
rs6545027	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs6545028	0.97[ASN][1000 genomes]
rs6545029	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6545030	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6545034	0.88[ASN][1000 genomes]
rs6545035	0.88[ASN][1000 genomes]
rs6545036	0.96[YRI][hapmap]
rs6705802	0.88[YRI][hapmap]
rs6712029	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6757206	0.92[ASN][1000 genomes]
rs72818493	0.98[ASN][1000 genomes]
rs72820405	0.88[ASN][1000 genomes]
rs72887649	0.98[ASN][1000 genomes]
rs7340322	0.90[ASN][1000 genomes]
rs7566239	0.96[YRI][hapmap]
rs7568960	0.92[ASN][1000 genomes]
rs7574125	0.82[ASN][1000 genomes]
rs7576964	0.92[YRI][hapmap]
rs7577237	0.96[YRI][hapmap]
rs7579932	0.96[YRI][hapmap]
rs7600794	1.00[YRI][hapmap]
rs7606104	1.00[YRI][hapmap]
rs9309152	0.86[ASN][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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10193072	FOXN2	cis	parietal	SCAN
rs10193072	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs10193072	PIGF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48506000-48539000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:48528000-48539200	Weak transcription	Primary T cells from cord blood	blood

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