Variant report

Variant	rs565761
Chromosome Location	chr5:43052246-43052247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43050678..43052352-chr5:43060897..43065115,3	MCF-7	breast:
2	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:
3	chr5:43048489..43050712-chr5:43051967..43053503,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf39-3	chr5:43052221-43052336	ucscGeneNc_uc003jnc_2

Variant related genes	Relation type
ENSG00000177738	Chromatin interaction
ENSG00000272144	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10522	0.87[ASN][1000 genomes]
rs12697439	0.84[ASN][1000 genomes]
rs13169690	0.86[ASN][1000 genomes]
rs13170208	0.82[ASN][1000 genomes]
rs13178479	0.82[ASN][1000 genomes]
rs1542369	0.82[ASN][1000 genomes]
rs1574407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160709	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs178415	0.91[ASN][1000 genomes]
rs1902101	0.81[AFR][1000 genomes]
rs222060	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2329994	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2329995	0.84[ASN][1000 genomes]
rs2548353	0.81[AFR][1000 genomes]
rs2548356	0.81[AFR][1000 genomes]
rs2603295	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2603636	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309914	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs316395	0.88[ASN][1000 genomes]
rs316396	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316400	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316402	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316403	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316404	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316406	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs316408	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316413	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316414	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs316416	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs316419	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs316422	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4033115	0.82[ASN][1000 genomes]
rs4092293	0.87[ASN][1000 genomes]
rs4092294	0.87[ASN][1000 genomes]
rs515970	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543569	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613825	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs643307	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6451660	0.82[ASN][1000 genomes]
rs6451661	0.82[ASN][1000 genomes]
rs6451662	0.82[ASN][1000 genomes]
rs6875214	0.85[ASN][1000 genomes]
rs724430	0.82[ASN][1000 genomes]
rs768441	0.87[ASN][1000 genomes]
rs9292862	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43043600-43052600	Weak transcription	A549	lung
2	chr5:43043600-43058200	Weak transcription	Gastric	stomach
3	chr5:43043600-43058200	Weak transcription	HSMMtube	muscle
4	chr5:43043600-43061600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:43043600-43063800	Weak transcription	Aorta	Aorta
6	chr5:43043600-43064000	Weak transcription	NHEK	skin
7	chr5:43043800-43054400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:43043800-43057400	Weak transcription	Primary B cells from cord blood	blood
9	chr5:43043800-43058000	Weak transcription	HepG2	liver
10	chr5:43043800-43061200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:43043800-43064000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:43044600-43052800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:43044800-43052600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:43044800-43052600	Weak transcription	Placenta	Placenta
15	chr5:43044800-43058200	Weak transcription	Lung	lung
16	chr5:43044800-43059400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:43044800-43064000	Weak transcription	Right Ventricle	heart
18	chr5:43044800-43064200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:43044800-43064400	Weak transcription	Brain Substantia Nigra	brain
20	chr5:43045000-43052400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr5:43045000-43061400	Weak transcription	NHLF	lung
22	chr5:43045000-43063800	Weak transcription	Adipose Nuclei	Adipose
23	chr5:43045000-43064200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:43045000-43064400	Weak transcription	Esophagus	oesophagus
25	chr5:43045200-43053400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:43045200-43053400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:43045400-43053400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:43045400-43058600	Weak transcription	Pancreas	Pancrea
29	chr5:43045400-43061400	Weak transcription	Hela-S3	cervix
30	chr5:43045400-43064200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:43045400-43066000	Weak transcription	Spleen	Spleen
32	chr5:43045600-43058800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:43045600-43061000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:43045600-43063600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:43045800-43053800	Weak transcription	Small Intestine	intestine
36	chr5:43046600-43052600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:43046600-43063800	Weak transcription	Left Ventricle	heart
38	chr5:43048200-43064200	Weak transcription	Psoas Muscle	Psoas
39	chr5:43048400-43052400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:43049200-43064000	Weak transcription	Fetal Stomach	stomach
41	chr5:43049400-43052600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:43049400-43061200	Weak transcription	HSMM	muscle
43	chr5:43049400-43061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:43049600-43052800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:43049800-43058200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:43049800-43064400	Weak transcription	Fetal Lung	lung
47	chr5:43050000-43053400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:43050000-43061400	Weak transcription	NH-A	brain
49	chr5:43050200-43058200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:43050600-43052600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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