Variant report

Variant	rs6792173
Chromosome Location	chr3:140025202-140025203
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	chr3:140022731..140026345-chr3:140027266..140029721,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1006877	0.89[GIH][hapmap]
rs1006878	0.89[GIH][hapmap]
rs1011758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026773	0.82[GIH][hapmap]
rs1026778	0.84[GIH][hapmap]
rs10513102	1.00[CHB][hapmap]
rs1154766	0.89[GIH][hapmap]
rs11708993	0.89[GIH][hapmap]
rs11714825	0.84[GIH][hapmap]
rs11719890	0.84[GIH][hapmap]
rs11915085	1.00[CHD][hapmap]
rs13066966	1.00[ASN][1000 genomes]
rs1351313	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.81[AMR][1000 genomes]
rs1383021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466461	0.84[AMR][1000 genomes]
rs1479868	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1479869	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[ASN][1000 genomes]
rs1479871	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531637	0.86[CEU][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17345403	0.89[GIH][hapmap]
rs2061929	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4327349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683485	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4683816	1.00[CHD][hapmap]
rs56105647	1.00[ASN][1000 genomes]
rs6765022	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs6766541	0.89[GIH][hapmap]
rs6770286	0.84[GIH][hapmap]
rs6770610	0.84[GIH][hapmap]
rs6784585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786128	0.89[GIH][hapmap]
rs6794692	0.84[GIH][hapmap]
rs6797652	0.89[GIH][hapmap]
rs6802157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810326	0.89[GIH][hapmap]
rs71314547	1.00[ASN][1000 genomes]
rs7611205	0.86[GIH][hapmap]
rs7630996	0.93[GIH][hapmap]
rs9289603	0.89[GIH][hapmap]
rs967861	0.81[CEU][hapmap]
rs9832534	0.91[GIH][hapmap]
rs9855259	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9864847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874598	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432486	chr3:139924092-140049121	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv4037	chr3:140020508-140032666	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	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
16	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6792173	CEP70	cis	parietal	SCAN
rs6792173	FOXL2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140018800-140034200	Weak transcription	Fetal Brain Male	brain
2	chr3:140021800-140028800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:140022800-140026800	Weak transcription	Ovary	ovary
4	chr3:140025000-140025400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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