Variant report

Variant	rs12659833
Chromosome Location	chr5:178553924-178553925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178486462..178489225-chr5:178551148..178554695,3	MCF-7	breast:
2	chr5:178549170..178551463-chr5:178552754..178555057,2	K562	blood:

Variant related genes	Relation type
ENSG00000177932	Chromatin interaction
ENSG00000087116	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2161170	0.83[ASN][1000 genomes]
rs2251105	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303643	0.81[ASN][1000 genomes]
rs3776810	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776811	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797590	0.83[ASN][1000 genomes]
rs3822591	0.83[ASN][1000 genomes]
rs4701048	0.83[ASN][1000 genomes]
rs4701050	0.83[ASN][1000 genomes]
rs6601020	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6860046	0.97[ASN][1000 genomes]
rs7718671	0.99[ASN][1000 genomes]
rs7722105	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
7	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv883222	chr5:178540975-178595870	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1016097	chr5:178544084-178866001	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1026968	chr5:178545479-178865895	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv537976	chr5:178545479-178865895	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv600495	chr5:178547567-178570914	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv600496	chr5:178552518-178752351	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 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	chr5:178527800-178559800	Weak transcription	HSMM	muscle
2	chr5:178538000-178560400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:178538200-178564600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:178545000-178555000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:178546000-178554000	Weak transcription	HSMMtube	muscle
6	chr5:178546800-178563200	Strong transcription	Adipose Nuclei	Adipose
7	chr5:178547000-178565400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:178547400-178560200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:178547600-178560200	Strong transcription	Placenta Amnion	Placenta Amnion
10	chr5:178547800-178560400	Strong transcription	Ovary	ovary
11	chr5:178548000-178559800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:178548200-178554800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:178548600-178570000	Weak transcription	NHDF-Ad	bronchial
14	chr5:178549400-178557000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:178549400-178590800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:178549600-178567400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:178550200-178556200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:178550400-178565600	Weak transcription	Esophagus	oesophagus
19	chr5:178550800-178559600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:178551200-178555800	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:178551200-178560200	Weak transcription	Fetal Intestine Small	intestine
22	chr5:178551400-178554400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:178551400-178559400	Weak transcription	Fetal Lung	lung
24	chr5:178551400-178559400	Strong transcription	Osteobl	bone
25	chr5:178551600-178582800	Weak transcription	Right Atrium	heart
26	chr5:178552000-178556800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
27	chr5:178552800-178554200	Strong transcription	Spleen	Spleen
28	chr5:178552800-178559600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:178552800-178559800	Weak transcription	Right Ventricle	heart
30	chr5:178552800-178566800	Strong transcription	Fetal Stomach	stomach
31	chr5:178553600-178554000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:178553600-178556000	Weak transcription	Gastric	stomach
33	chr5:178553600-178559600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr5:178553800-178554600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:178553800-178554800	Weak transcription	Aorta	Aorta
36	chr5:178553800-178560000	Strong transcription	NHLF	lung
37	chr5:178553800-178569000	Weak transcription	Liver	Liver

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