Variant report

Variant	rs6788712
Chromosome Location	chr3:118892533-118892534
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	chr3:118877630..118879660-chr3:118892523..118895132,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12630657	0.81[ASN][1000 genomes]
rs12631542	0.84[ASN][1000 genomes]
rs12636680	0.84[ASN][1000 genomes]
rs13077000	0.82[ASN][1000 genomes]
rs13079334	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13086223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34504080	0.90[ASN][1000 genomes]
rs4077930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4618215	0.90[ASN][1000 genomes]
rs56213565	0.84[ASN][1000 genomes]
rs62273474	0.81[ASN][1000 genomes]
rs6768478	0.87[ASN][1000 genomes]
rs6784018	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs7619798	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829692	chr3:118727772-118901711	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118884000-118914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:118890200-118894400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:118890200-118900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:118890400-118894800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:118891800-118892800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:118892000-118892600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:118892000-118893000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:118892200-118892600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
9	chr3:118892200-118892600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:118892200-118892600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:118892200-118892600	Enhancers	Fetal Heart	heart
12	chr3:118892200-118892600	Enhancers	Placenta	Placenta
13	chr3:118892200-118892600	Enhancers	K562	blood
14	chr3:118892200-118893200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:118892400-118892600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
16	chr3:118892400-118892600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:118892400-118892600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:118892400-118892800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:118892400-118893000	Active TSS	Placenta Amnion	Placenta Amnion
20	chr3:118892400-118893000	Active TSS	Stomach Mucosa	stomach
21	chr3:118892400-118893200	Flanking Active TSS	A549	lung
22	chr3:118892400-118893400	Bivalent/Poised TSS	Fetal Stomach	stomach

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