Variant report

Variant	rs58575540
Chromosome Location	chr5:179742990-179742991
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179627950..179628952-chr5:179742140..179743347,3	K562	blood:
2	chr5:179554088..179554742-chr5:179742467..179743013,2	MCF-7	breast:
3	chr5:179739299..179743379-chr5:179893176..179898905,6	MCF-7	breast:
4	chr5:179739339..179743235-chr5:179757984..179764634,9	MCF-7	breast:
5	chr5:179692323..179695194-chr5:179741562..179744368,2	K562	blood:
6	chr5:179740156..179743106-chr5:179752395..179754766,3	MCF-7	breast:
7	chr5:179741922..179743146-chr5:179755337..179756583,4	MCF-7	breast:
8	chr5:179714082..179715807-chr5:179741478..179743115,2	MCF-7	breast:
9	chr5:179742474..179743351-chr5:179897684..179898604,3	MCF-7	breast:
10	chr5:179719970..179720873-chr5:179742427..179743336,6	MCF-7	breast:
11	chr5:179718624..179722005-chr5:179739945..179743525,7	MCF-7	breast:
12	chr5:179717535..179723990-chr5:179738269..179745292,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000248367	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12654592	0.87[AMR][1000 genomes]
rs12655822	0.87[AMR][1000 genomes]
rs2042224	0.91[AMR][1000 genomes]
rs34735703	0.87[AMR][1000 genomes]
rs4323198	0.87[AMR][1000 genomes]
rs58312286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58437941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58821651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58979087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60396605	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60634512	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73349659	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73349662	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7447624	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
6	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
7	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 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	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
2	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
3	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:179720800-179743600	Weak transcription	Right Atrium	heart
5	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:179721000-179743000	Weak transcription	Spleen	Spleen
7	chr5:179726800-179750600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:179728600-179761400	Weak transcription	Aorta	Aorta
14	chr5:179728800-179750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:179729600-179743200	Weak transcription	HSMM	muscle
16	chr5:179730800-179750800	Weak transcription	HSMMtube	muscle
17	chr5:179731600-179755600	Weak transcription	Fetal Brain Female	brain
18	chr5:179732200-179750800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:179732800-179751200	Weak transcription	Adipose Nuclei	Adipose
20	chr5:179733600-179744800	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:179736800-179751800	Weak transcription	Left Ventricle	heart
22	chr5:179737400-179750000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:179737600-179746200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:179737600-179750800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:179738000-179758000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:179738200-179746200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:179738200-179755600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:179738600-179745200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:179738800-179743200	Weak transcription	Brain Anterior Caudate	brain
30	chr5:179738800-179743600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:179738800-179748600	Weak transcription	Lung	lung
32	chr5:179739000-179743200	Weak transcription	Brain Angular Gyrus	brain
33	chr5:179739000-179743200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:179739000-179743200	Weak transcription	A549	lung
35	chr5:179739600-179761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:179740000-179744800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:179740400-179757400	Weak transcription	NHLF	lung
38	chr5:179740600-179757600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:179741000-179750600	Strong transcription	Osteobl	bone
40	chr5:179741200-179746200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:179741200-179750400	Weak transcription	Esophagus	oesophagus
42	chr5:179741200-179754000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:179741400-179743000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:179741400-179743200	Weak transcription	Placenta	Placenta
45	chr5:179741400-179743200	Weak transcription	Ovary	ovary
46	chr5:179741400-179743400	Weak transcription	Gastric	stomach
47	chr5:179741400-179744000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:179741400-179744400	Strong transcription	NH-A	brain
49	chr5:179741400-179746800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr5:179741400-179746800	Strong transcription	Fetal Stomach	stomach

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