Variant report

Variant	rs923397
Chromosome Location	chr12:48720392-48720393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48720103..48722242-chr12:48743516..48745701,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000167528	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1061986	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10875753	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs1107654	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168428	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs11168437	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs11168464	0.80[EUR][1000 genomes]
rs11168468	0.86[EUR][1000 genomes]
rs11168474	0.85[EUR][1000 genomes]
rs11168484	0.87[EUR][1000 genomes]
rs12828309	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12829841	0.87[EUR][1000 genomes]
rs1387259	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1387260	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1476607	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs1489108	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1542707	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1552550	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2054905	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2409003	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409004	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450996	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2468943	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2468946	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2468949	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634676	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634678	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634680	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634681	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634682	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634684	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]
rs2634686	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634688	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634689	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634691	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634692	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634693	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634694	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2732441	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732448	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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732453	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732457	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732461	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2732462	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732466	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]
rs2732479	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732480	0.95[GIH][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs2732481	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732484	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];0.95[EUR][1000 genomes]
rs2732486	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2956703	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2956710	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34286639	0.87[EUR][1000 genomes]
rs6580662	0.86[EUR][1000 genomes]
rs7297824	0.92[CEU][hapmap]
rs7301003	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs7307566	0.83[EUR][1000 genomes]
rs7315820	0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7486941	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs7487682	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap]
rs7959684	1.00[CHD][hapmap]
rs7966829	0.85[EUR][1000 genomes]
rs8716	1.00[CHD][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs923397	H1FNT	cis	Muscle Skeletal	GTEx
rs923397	ZNF641	cis	cerebellum	SCAN
rs923397	FKBP11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48720200-48720400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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