Variant report

Variant	rs28525971
Chromosome Location	chr3:179123669-179123670
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	chr3:179122316..179126599-chr3:179129237..179132058,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MFN1-2	chr3:179123236-179123732	ENSG00000272699.1

Variant related genes	Relation type
ENSG00000114450	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1061318	0.89[AFR][1000 genomes]
rs28458281	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56231352	1.00[ASN][1000 genomes]
rs58167439	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60118786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735185	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768421	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769014	1.00[ASN][1000 genomes]
rs6791839	0.89[AFR][1000 genomes]
rs6792924	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043415	1.00[ASN][1000 genomes]
rs7626133	0.81[AFR][1000 genomes]
rs9877546	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877945	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
4	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
5	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
8	chr3:179098400-179125000	Weak transcription	Ovary	ovary
9	chr3:179101600-179125800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:179101800-179125800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:179102200-179126400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:179105000-179131200	Weak transcription	Fetal Heart	heart
14	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
16	chr3:179109400-179124600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:179110800-179133400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:179111600-179128600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:179111600-179138600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
21	chr3:179112000-179125000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:179112000-179133000	Weak transcription	Brain Angular Gyrus	brain
23	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
24	chr3:179112200-179136400	Weak transcription	Brain Substantia Nigra	brain
25	chr3:179112200-179138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:179112200-179142600	Weak transcription	Esophagus	oesophagus
27	chr3:179112600-179131200	Weak transcription	NHEK	skin
28	chr3:179112800-179144200	Weak transcription	A549	lung
29	chr3:179113800-179146800	Weak transcription	Gastric	stomach
30	chr3:179114200-179139200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:179115000-179130000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:179115600-179139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:179115800-179136600	Weak transcription	Pancreas	Pancrea
34	chr3:179116200-179125000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:179116800-179124200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:179116800-179125600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:179117200-179125800	Strong transcription	Dnd41	blood
38	chr3:179117600-179125800	Strong transcription	HSMM	muscle
39	chr3:179117800-179123800	Strong transcription	Osteobl	bone
40	chr3:179117800-179125600	Strong transcription	Primary B cells from cord blood	blood
41	chr3:179118000-179137600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:179118800-179125200	Weak transcription	GM12878-XiMat	blood
43	chr3:179118800-179128000	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:179119800-179124400	Strong transcription	Fetal Lung	lung
45	chr3:179119800-179126400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:179119800-179131600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:179120000-179124000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:179120000-179133400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:179120400-179125200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:179120600-179125800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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