Variant report

Variant	rs72870609
Chromosome Location	chr3:54666347-54666348
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54657347..54660339-chr3:54665865..54667406,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRTM1-3	chr3:54666151-54666883	NONHSAT090017

Variant related genes	Relation type
ENSG00000229806	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs58865225	0.89[AFR][1000 genomes]
rs72868888	0.84[AFR][1000 genomes]
rs72870607	1.00[AMR][1000 genomes]
rs72870636	0.88[AFR][1000 genomes]
rs72870668	1.00[AMR][1000 genomes]
rs72870684	1.00[AMR][1000 genomes]
rs72870700	1.00[AMR][1000 genomes]
rs72872241	1.00[AMR][1000 genomes]
rs72872252	1.00[AMR][1000 genomes]
rs72872301	1.00[AMR][1000 genomes]
rs72874221	1.00[AMR][1000 genomes]
rs72874223	1.00[AMR][1000 genomes]
rs72874234	1.00[AMR][1000 genomes]
rs72874238	1.00[AMR][1000 genomes]
rs73844118	0.89[AFR][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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:54660400-54666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:54663000-54667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:54663200-54667400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:54663800-54667400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:54663800-54667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:54664600-54666400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:54664600-54667200	Weak transcription	HMEC	breast
11	chr3:54664800-54666400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:54665000-54666400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:54665200-54666400	Enhancers	Fetal Brain Male	brain
14	chr3:54665200-54667000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr3:54665200-54667200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:54665200-54667800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:54665200-54672800	Weak transcription	Right Atrium	heart
18	chr3:54665400-54667000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:54665400-54668200	Enhancers	Brain Germinal Matrix	brain
20	chr3:54665600-54666600	Enhancers	Fetal Brain Female	brain
21	chr3:54665800-54666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:54665800-54667600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:54666000-54667000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:54666200-54667800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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