Variant report

Variant	rs2730931
Chromosome Location	chr12:38941429-38941430
allele	A/G
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	E2F4	chr12:38941371-38941717	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr12:38941417-38941756	MCF10A-Er-Src	breast:	n/a	chr12:38941556-38941565 chr12:38941555-38941564
3	FOS	chr12:38941392-38941802	MCF10A-Er-Src	breast:	n/a	chr12:38941610-38941622 chr12:38941556-38941563 chr12:38941556-38941564 chr12:38941559-38941566 chr12:38941612-38941620
4	FOS	chr12:38941330-38941821	MCF10A-Er-Src	breast:	n/a	chr12:38941610-38941622 chr12:38941556-38941563 chr12:38941556-38941564 chr12:38941559-38941566 chr12:38941612-38941620
5	MYC	chr12:38941427-38941742	MCF10A-Er-Src	breast:	n/a	chr12:38941556-38941565 chr12:38941612-38941621 chr12:38941555-38941564
6	FOS	chr12:38941404-38941756	MCF10A-Er-Src	breast:	n/a	chr12:38941610-38941622 chr12:38941556-38941563 chr12:38941556-38941564 chr12:38941559-38941566 chr12:38941612-38941620
7	STAT3	chr12:38941378-38941756	MCF10A-Er-Src	breast:	n/a	chr12:38941556-38941565 chr12:38941555-38941564
8	FOS	chr12:38941329-38942042	MCF10A-Er-Src	breast:	n/a	chr12:38941610-38941622 chr12:38941556-38941563 chr12:38941556-38941564 chr12:38941559-38941566 chr12:38941612-38941620
9	STAT3	chr12:38941401-38941782	MCF10A-Er-Src	breast:	n/a	chr12:38941556-38941565 chr12:38941555-38941564

Variant related genes	Relation type
ENSG00000258119	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10875959	0.86[ASN][1000 genomes]
rs10875962	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs10875963	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs11168552	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168979	0.83[ASN][1000 genomes]
rs11169095	0.86[ASN][1000 genomes]
rs12309958	0.85[ASN][1000 genomes]
rs12318974	0.86[ASN][1000 genomes]
rs12322362	0.99[ASN][1000 genomes]
rs12580227	0.87[ASN][1000 genomes]
rs1472657	0.83[ASN][1000 genomes]
rs1502631	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1827459	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1847181	0.81[ASN][1000 genomes]
rs2101370	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs2264357	0.85[ASN][1000 genomes]
rs2630779	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653739	0.90[ASN][1000 genomes]
rs2653757	0.85[ASN][1000 genomes]
rs2653762	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2653770	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2653777	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730891	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2730911	1.00[CEU][hapmap]
rs2730923	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2730938	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4238079	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767968	0.86[ASN][1000 genomes]
rs7957523	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs7980889	0.86[ASN][1000 genomes]
rs923200	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9645814	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs9805091	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv898992	chr12:38106133-38959053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1047388	chr12:38169669-38949760	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv826332	chr12:38442547-38958438	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1046439	chr12:38453609-38956518	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv541475	chr12:38453609-38956518	Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1039179	chr12:38453609-39029275	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv541476	chr12:38453609-39029275	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv916679	chr12:38805678-38963660	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1048325	chr12:38820721-38959645	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1040304	chr12:38908242-38995786	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1046817	chr12:38909036-38995330	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv469358	chr12:38919524-38989405	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv558582	chr12:38919524-38989405	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38941000-38941800	Enhancers	Hela-S3	cervix
2	chr12:38941200-38942000	Enhancers	HMEC	breast
3	chr12:38941200-38942600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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