Variant report

Variant	rs2242313
Chromosome Location	chr8:120102529-120102530
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:120098923..120102806-chr8:120218978..120221966,5	MCF-7	breast:
2	chr8:120101259..120103990-chr8:120252678..120255585,2	MCF-7	breast:
3	chr8:120096968..120103471-chr8:120218555..120222838,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147676	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1156545	0.92[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1158945	0.82[JPT][hapmap]
rs11994775	0.82[JPT][hapmap]
rs13248274	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13248569	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13257113	0.88[ASN][1000 genomes]
rs13262749	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1351952	0.82[JPT][hapmap]
rs1351954	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1364709	0.82[CEU][hapmap]
rs1385492	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1385493	0.89[CEU][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes]
rs1385496	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1385498	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs1425055	0.82[CEU][hapmap]
rs1485293	0.82[JPT][hapmap]
rs1872424	0.85[CEU][hapmap]
rs1905775	0.81[CHD][hapmap]
rs1961996	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2113885	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2247769	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2432965	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2450061	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450065	0.82[JPT][hapmap]
rs2450067	0.82[JPT][hapmap]
rs2450068	0.82[JPT][hapmap]
rs2450069	0.82[JPT][hapmap]
rs2450072	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2450080	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465383	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap]
rs2465385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465387	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465390	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2465392	0.82[JPT][hapmap]
rs2465393	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465394	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465395	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465403	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2465404	0.82[JPT][hapmap]
rs2468177	0.82[CEU][hapmap]
rs2468181	0.82[CEU][hapmap]
rs2468182	0.82[CEU][hapmap]
rs6469811	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6994271	0.88[ASN][1000 genomes]
rs7388447	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7813952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7827224	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs996789	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2242313	NOV	cis	cerebellum	SCAN
rs2242313	SAMD12	cis	parietal	SCAN
rs2242313	MAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120099000-120103600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr8:120099200-120106000	Weak transcription	NHLF	lung

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