Variant report

Variant	rs11249668
Chromosome Location	chr5:179543481-179543482
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	chr5:179542665..179545616-chr5:179718276..179721972,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050748	Chromatin interaction
ENSG00000248367	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12656413	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12657718	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17080045	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4356995	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56346373	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72813632	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv1021754	chr5:179522070-179547579	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1033460	chr5:179526789-179565253	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1020038	chr5:179526789-179566589	Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv883287	chr5:179526789-179584778	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv883288	chr5:179537727-179608656	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 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	chr5:179536000-179543600	Weak transcription	Fetal Brain Female	brain
2	chr5:179536200-179554200	Weak transcription	Brain Germinal Matrix	brain
3	chr5:179537800-179546000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:179539000-179545000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:179542600-179544000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:179542800-179543800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:179542800-179543800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:179543000-179543800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179543000-179543800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:179543000-179544000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:179543000-179544000	Enhancers	Brain Hippocampus Middle	brain
12	chr5:179543000-179544000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr5:179543000-179544400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:179543200-179543800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr5:179543200-179543800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:179543200-179543800	Enhancers	Brain Anterior Caudate	brain
17	chr5:179543200-179544000	Enhancers	Brain Angular Gyrus	brain
18	chr5:179543200-179544400	Enhancers	Brain Substantia Nigra	brain
19	chr5:179543200-179545200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:179543400-179543800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:179543400-179544000	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:179543400-179553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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