Variant report

Variant	rs12299772
Chromosome Location	chr12:86651485-86651486
allele	A/C
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	POLR2A	chr12:86651352-86651510	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:86651437-86651660	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MGAT4C	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11103901	1.00[AFR][1000 genomes]
rs11103902	1.00[AFR][1000 genomes]
rs11103905	1.00[AFR][1000 genomes]
rs11103906	1.00[AFR][1000 genomes]
rs11103907	1.00[AFR][1000 genomes]
rs12298208	1.00[AFR][1000 genomes]
rs12298422	1.00[AFR][1000 genomes]
rs12299950	0.88[AFR][1000 genomes]
rs12300410	0.84[AFR][1000 genomes]
rs12303146	0.88[AFR][1000 genomes]
rs12305480	0.88[AFR][1000 genomes]
rs12306455	1.00[AFR][1000 genomes]
rs12306583	0.94[AFR][1000 genomes]
rs12308711	0.88[AFR][1000 genomes]
rs12309297	1.00[AFR][1000 genomes]
rs12311208	0.88[AFR][1000 genomes]
rs12315031	1.00[AFR][1000 genomes]
rs12316205	0.88[AFR][1000 genomes]
rs12318124	0.88[AFR][1000 genomes]
rs12318727	0.88[AFR][1000 genomes]

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	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86644200-86655400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:86650200-86653600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:86650200-86655400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:86650200-86658200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:86650200-86658400	Weak transcription	Left Ventricle	heart
6	chr12:86651000-86651600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:86651000-86651600	Enhancers	Fetal Heart	heart
8	chr12:86651000-86655000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:86651400-86654000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:86651400-86655000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:86651400-86658200	Weak transcription	Brain Germinal Matrix	brain

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