Variant report

Variant	rs16945916
Chromosome Location	chr16:48201432-48201433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:48201392-48201480	MCF-7	breast:	n/a	n/a
2	POLR2A	chr16:48201309-48201496	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000261538	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10163354	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10163462	1.00[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861031	1.00[CEU][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861127	0.83[ASW][hapmap];0.83[CHD][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs11863133	0.93[ASN][1000 genomes]
rs11863233	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs11863236	0.85[CHD][hapmap];0.93[ASN][1000 genomes]
rs11863325	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866251	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866312	0.93[ASN][1000 genomes]
rs11866529	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs13336264	0.86[ASN][1000 genomes]
rs16945917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945919	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945972	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs16945974	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs17743256	1.00[ASN][1000 genomes]
rs28376623	0.93[ASN][1000 genomes]
rs28503414	0.93[ASN][1000 genomes]
rs28605399	0.85[ASN][1000 genomes]
rs28626252	0.93[ASN][1000 genomes]
rs28654935	0.93[ASN][1000 genomes]
rs28684834	0.93[ASN][1000 genomes]
rs28696036	0.93[ASN][1000 genomes]
rs41280939	1.00[ASN][1000 genomes]
rs5017203	0.93[ASN][1000 genomes]
rs57912486	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058522	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058526	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500339	0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7184831	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187233	1.00[ASN][1000 genomes]
rs7191844	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203695	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs7206909	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs73540901	0.93[ASN][1000 genomes]
rs73542903	0.93[ASN][1000 genomes]
rs73542904	0.93[ASN][1000 genomes]
rs73546434	0.85[ASN][1000 genomes]
rs73546437	0.85[ASN][1000 genomes]
rs73546439	0.85[ASN][1000 genomes]
rs74018298	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs74018300	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046814	0.93[ASN][1000 genomes]
rs8047091	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs8047397	0.85[ASN][1000 genomes]
rs8050120	1.00[ASN][1000 genomes]
rs8051016	0.85[CHD][hapmap];0.93[ASN][1000 genomes]
rs8051205	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs8055128	0.85[ASN][1000 genomes]
rs8056100	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs8056143	0.85[ASN][1000 genomes]
rs8057475	0.93[ASN][1000 genomes]
rs8060696	0.85[ASN][1000 genomes]
rs8060722	0.85[ASN][1000 genomes]
rs957881	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9932850	0.93[ASN][1000 genomes]
rs9939742	1.00[CHD][hapmap]
rs9941123	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16945916	LONP2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48192800-48204000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:48198800-48204800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr16:48199200-48226600	Weak transcription	Spleen	Spleen
4	chr16:48199600-48202000	Weak transcription	Adipose Nuclei	Adipose
5	chr16:48200200-48209000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:48200400-48201600	Enhancers	HepG2	liver
7	chr16:48201200-48201800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr16:48201200-48202800	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr16:48201400-48202800	Enhancers	Primary monocytes fromperipheralblood	blood

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