Variant report

Variant	rs6548605
Chromosome Location	chr3:79058782-79058783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:79056426..79058913-chr3:79066777..79068329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11127638	0.86[EUR][1000 genomes]
rs11923198	0.86[EUR][1000 genomes]
rs12495750	0.86[EUR][1000 genomes]
rs13096526	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1349023	0.86[EUR][1000 genomes]
rs1349024	0.86[EUR][1000 genomes]
rs1374883	0.86[EUR][1000 genomes]
rs1374885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1374886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1374887	0.86[EUR][1000 genomes]
rs1374888	0.86[EUR][1000 genomes]
rs1374889	0.86[EUR][1000 genomes]
rs1900663	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1947154	0.86[EUR][1000 genomes]
rs2871747	0.86[EUR][1000 genomes]
rs4680946	1.00[EUR][1000 genomes]
rs6548603	0.86[EUR][1000 genomes]
rs6548604	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6548606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6774082	0.86[EUR][1000 genomes]
rs6788693	0.86[EUR][1000 genomes]
rs6797152	0.86[EUR][1000 genomes]
rs6804234	1.00[EUR][1000 genomes]
rs7625043	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7646169	0.86[EUR][1000 genomes]
rs9845900	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834745	chr3:79055426-79227937	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:79040800-79062000	Weak transcription	Ovary	ovary
2	chr3:79044600-79061600	Weak transcription	Fetal Kidney	kidney
3	chr3:79044800-79064600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:79052000-79059000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:79052800-79060000	Weak transcription	Fetal Lung	lung
6	chr3:79053200-79061200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:79053200-79061400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:79054200-79059200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:79054200-79061000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:79054400-79059200	Weak transcription	Fetal Brain Female	brain
11	chr3:79054400-79066600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:79054600-79059000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:79054600-79060200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:79054600-79061000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:79054600-79061800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:79054600-79062000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:79054600-79064600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:79055600-79061000	Weak transcription	Aorta	Aorta
19	chr3:79055600-79061400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:79055600-79061400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:79055600-79062000	Weak transcription	NHDF-Ad	bronchial
22	chr3:79055800-79061400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:79056200-79060200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:79056200-79062000	Weak transcription	Osteobl	bone
25	chr3:79056400-79059400	Enhancers	Brain Anterior Caudate	brain
26	chr3:79056600-79060400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:79057000-79059400	Weak transcription	A549	lung
28	chr3:79057400-79058800	Weak transcription	HepG2	liver
29	chr3:79057400-79059000	Weak transcription	Brain Angular Gyrus	brain
30	chr3:79057400-79061200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:79057400-79061600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:79057600-79061400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:79057600-79061800	Enhancers	Fetal Brain Male	brain
34	chr3:79058200-79060600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:79058600-79059000	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:79058600-79059000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:79058600-79064600	Enhancers	Brain Hippocampus Middle	brain

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