Variant report

Variant	rs987486
Chromosome Location	chr3:140049319-140049320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:41399109..41402008-chr3:140047432..140050412,2	MCF-7	breast:
2	chr17:41380303..41382086-chr3:140048912..140050412,2	K562	blood:
3	chr3:140048554..140050507-chr3:140068162..140070278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236383	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1006877	0.85[CEU][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs1006878	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1026775	0.82[GIH][hapmap]
rs1154765	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1154766	0.82[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706485	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12636954	1.00[JPT][hapmap]
rs1479874	0.83[ASN][1000 genomes]
rs1479877	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1479879	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1564395	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1564397	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16850133	1.00[JPT][hapmap]
rs17345403	0.83[GIH][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs1871497	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1964547	0.82[EUR][1000 genomes]
rs35501742	0.83[ASN][1000 genomes]
rs3925729	0.88[ASN][1000 genomes]
rs3947733	0.80[EUR][1000 genomes]
rs4142786	1.00[JPT][hapmap]
rs6414346	0.82[EUR][1000 genomes]
rs6762256	0.92[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6765022	0.82[GIH][hapmap]
rs6766533	0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6766541	0.83[GIH][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs6786128	0.83[GIH][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs6786368	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6797652	0.83[GIH][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs6810326	0.83[GIH][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs7610342	1.00[JPT][hapmap]
rs7610675	0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7611205	0.85[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.85[EUR][1000 genomes]
rs7624142	0.82[AMR][1000 genomes]
rs7630996	0.85[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7631243	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7638929	1.00[JPT][hapmap]
rs7653676	0.81[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs879716	0.83[ASW][hapmap]
rs9289603	0.83[GIH][hapmap]
rs9832534	0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9837940	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9858505	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs9871764	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv829740	chr3:139925767-140106169	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv460867	chr3:140007294-140180563	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv591861	chr3:140007294-140180563	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv818169	chr3:140014763-140182046	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1001430	chr3:140016999-140186498	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv998953	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv536731	chr3:140017168-140186984	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv829741	chr3:140021063-140183294	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1004500	chr3:140021594-140189148	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs987486	FOXL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140043000-140068600	Weak transcription	HSMMtube	muscle
2	chr3:140046400-140055400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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