Variant report

Variant	rs239518
Chromosome Location	chr6:80653373-80653374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80653198..80656160-chr6:80712595..80714599,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112742	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs151668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs151670	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs163983	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs184672	0.99[AFR][1000 genomes]
rs239519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs239530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs239531	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343621	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343622	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343624	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343630	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343633	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343634	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs343690	1.00[AMR][1000 genomes]
rs343703	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs346364	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs346365	0.97[AFR][1000 genomes];1.00[AMR][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3475140	chr6:80592690-80679283	Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3475142	chr6:80592789-80679132	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80618400-80656000	Weak transcription	Aorta	Aorta
2	chr6:80632000-80654800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:80640200-80654800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:80650800-80653800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:80651000-80653400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:80651000-80653800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:80651000-80655200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:80651000-80655600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:80651400-80653400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:80652000-80654400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:80652000-80654800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:80652000-80654800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:80652000-80655800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:80652000-80656200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:80652200-80655600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
16	chr6:80652400-80653600	Enhancers	Brain Anterior Caudate	brain
17	chr6:80652400-80653600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr6:80652800-80653800	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:80653000-80653400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:80653000-80653400	Enhancers	HMEC	breast
21	chr6:80653000-80653600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:80653000-80653600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:80653000-80653600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:80653000-80653600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:80653000-80653800	Transcr. at gene 5' and 3'	Thymus	Thymus
26	chr6:80653000-80653800	Transcr. at gene 5' and 3'	Dnd41	blood
27	chr6:80653000-80654800	Enhancers	Fetal Brain Female	brain
28	chr6:80653000-80655000	Enhancers	Fetal Brain Male	brain
29	chr6:80653000-80655600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:80653200-80653400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:80653200-80653400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:80653200-80653400	Bivalent Enhancer	Psoas Muscle	Psoas
33	chr6:80653200-80653600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:80653200-80653800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:80653200-80654400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:80653200-80655800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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