Variant report

Variant	rs62404953
Chromosome Location	chr5:179770757-179770758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179769448..179771276-chr5:179896602..179898870,2	MCF-7	breast:
2	chr5:179770572..179772662-chr5:179890635..179892698,2	MCF-7	breast:
3	chr5:179769960..179774834-chr5:179776858..179780892,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1078646	0.98[ASN][1000 genomes]
rs1559114	0.99[ASN][1000 genomes]
rs17080196	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17080199	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303012	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4235511	0.97[ASN][1000 genomes]
rs4566752	0.99[ASN][1000 genomes]
rs4700736	0.97[ASN][1000 genomes]
rs4700943	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404950	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62404956	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404958	0.97[ASN][1000 genomes]
rs62404959	0.98[ASN][1000 genomes]
rs62406364	0.92[ASN][1000 genomes]
rs6601110	0.91[ASN][1000 genomes]
rs6859159	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6864729	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6870028	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6871454	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6874176	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6884276	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6899097	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72811045	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72811049	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9686940	0.91[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	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
11	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv984575	chr5:179759624-179791220	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179757000-179779000	Weak transcription	Esophagus	oesophagus
2	chr5:179763000-179771400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:179764000-179778800	Weak transcription	Pancreas	Pancrea
4	chr5:179765000-179771000	Weak transcription	Left Ventricle	heart
5	chr5:179765000-179775000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:179766800-179771800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:179768200-179772200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:179768800-179775400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:179769400-179772400	Enhancers	Fetal Muscle Trunk	muscle
10	chr5:179770000-179770800	Flanking Active TSS	Osteobl	bone
11	chr5:179770000-179771000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:179770000-179771000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:179770000-179771000	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr5:179770000-179771000	Enhancers	Fetal Kidney	kidney
15	chr5:179770000-179771200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:179770000-179771200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:179770000-179771200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:179770000-179771200	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr5:179770000-179771400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:179770000-179771400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr5:179770000-179771400	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr5:179770000-179771400	Enhancers	Fetal Stomach	stomach
23	chr5:179770000-179771400	Enhancers	NHLF	lung
24	chr5:179770000-179771600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:179770000-179771600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:179770000-179771600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr5:179770000-179771600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr5:179770000-179771600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr5:179770000-179771600	Enhancers	Adipose Nuclei	Adipose
30	chr5:179770000-179771600	Enhancers	Fetal Brain Male	brain
31	chr5:179770000-179771600	Enhancers	Fetal Lung	lung
32	chr5:179770000-179771600	Enhancers	Ovary	ovary
33	chr5:179770000-179771800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:179770000-179772400	Enhancers	Fetal Muscle Leg	muscle
35	chr5:179770000-179775600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:179770200-179770800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr5:179770200-179770800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:179770200-179770800	Flanking Active TSS	Fetal Brain Female	brain
39	chr5:179770200-179771000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:179770200-179771200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:179770200-179771200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:179770200-179771200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:179770200-179771200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr5:179770200-179771200	Flanking Active TSS	NHDF-Ad	bronchial
45	chr5:179770200-179771400	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr5:179770200-179771400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr5:179770200-179771400	Enhancers	HSMMtube	muscle
48	chr5:179770200-179771400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
49	chr5:179770200-179771600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:179770400-179771000	Weak transcription	Lung	lung

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