Variant report

Variant	rs11539416
Chromosome Location	chr3:179115649-179115650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179064557..179067034-chr3:179115322..179117988,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MFN1-1	chr3:179115405-179115710	ENSG00000242539.1
2	lnc-GNB4-1	chr3:179113877-179115965	ENSG00000269728.1
3	lnc-MFN1-1	chr3:179114749-179115710	ENSG00000242539.2
4	lnc-MFN1-1	chr3:179115121-179115781	ENSG00000242539.2
5	lnc-MFN1-1	chr3:179115496-179115729	ENSG00000242539.2

No data

Variant related genes	Relation type
ENSG00000171109	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1061751	0.83[ASN][1000 genomes]
rs10937003	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714353	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715130	0.84[ASN][1000 genomes]
rs11715227	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11717019	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11720405	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632708	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12634184	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13327561	0.88[ASN][1000 genomes]
rs2111278	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287212	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287311	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28588445	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806687	0.85[ASN][1000 genomes]
rs58230199	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60388496	0.86[ASN][1000 genomes]
rs62408893	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62410442	0.84[ASN][1000 genomes]
rs62410443	0.84[ASN][1000 genomes]
rs62410444	0.84[ASN][1000 genomes]
rs62410445	0.84[ASN][1000 genomes]
rs6774135	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6794532	0.84[ASN][1000 genomes]
rs73172210	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610174	0.84[ASN][1000 genomes]
rs7642257	0.82[ASN][1000 genomes]
rs7644501	0.84[ASN][1000 genomes]
rs9790192	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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:120 , 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	chr3:179066800-179118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:179070600-179120000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
6	chr3:179081600-179120400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
8	chr3:179087200-179122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:179087600-179120000	Weak transcription	Right Ventricle	heart
10	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
13	chr3:179098400-179120200	Weak transcription	Lung	lung
14	chr3:179098400-179125000	Weak transcription	Ovary	ovary
15	chr3:179099400-179119400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:179099600-179119600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:179101600-179125800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:179101800-179115800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:179101800-179119200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:179101800-179125800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:179102200-179126400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:179103200-179120600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:179103400-179115800	Strong transcription	Adipose Nuclei	Adipose
25	chr3:179103400-179115800	Strong transcription	Fetal Thymus	thymus
26	chr3:179103400-179116200	Strong transcription	HSMM	muscle
27	chr3:179103400-179116400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:179103400-179119000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:179103600-179120200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:179103800-179116400	Strong transcription	Primary T cells from cord blood	blood
31	chr3:179105000-179131200	Weak transcription	Fetal Heart	heart
32	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
34	chr3:179106800-179117000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:179106800-179119000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:179107000-179116800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:179108000-179116000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:179108400-179123400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:179108600-179116000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:179108600-179116600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr3:179109400-179117600	Weak transcription	Hela-S3	cervix
42	chr3:179109400-179124600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:179110000-179118800	Strong transcription	GM12878-XiMat	blood
44	chr3:179110000-179123400	Strong transcription	HUVEC	blood vessel
45	chr3:179110800-179116000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:179110800-179133400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:179111000-179115800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:179111200-179116400	Strong transcription	Dnd41	blood
49	chr3:179111600-179116000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:179111600-179128600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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