Variant report

Variant	rs60388708
Chromosome Location	chr5:179490597-179490598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179490013..179492341-chr5:179495671..179497729,3	MCF-7	breast:
2	chr5:179489682..179493173-chr5:179498595..179500397,3	MCF-7	breast:
3	chr5:179488708..179492328-chr5:179496278..179499122,4	K562	blood:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10067073	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10072792	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12514260	0.86[AFR][1000 genomes]
rs12516233	0.86[AFR][1000 genomes]
rs12516629	0.92[AFR][1000 genomes]
rs12521819	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13354862	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478989	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57144908	0.86[AFR][1000 genomes]
rs58286692	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59150995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59668758	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60044157	0.90[EUR][1000 genomes]
rs73350172	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
4	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
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	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
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
3	chr5:179476000-179497800	Weak transcription	Lung	lung
4	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
5	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:179477400-179495000	Weak transcription	Gastric	stomach
7	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
8	chr5:179478800-179493800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
10	chr5:179480600-179494000	Weak transcription	Fetal Lung	lung
11	chr5:179480600-179496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:179481200-179496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:179481600-179494600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:179484400-179495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:179484800-179494000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:179485000-179493200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:179486600-179494000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:179486800-179495200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:179486800-179496800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:179487000-179495000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:179487400-179494600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:179487800-179494000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:179488400-179494000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:179488400-179494200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:179488400-179494400	Weak transcription	Fetal Brain Male	brain
28	chr5:179488600-179494000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:179488600-179494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:179488600-179494200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:179488600-179496800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:179488800-179490800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:179488800-179491200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:179488800-179491600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:179488800-179494200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:179489000-179490800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:179489000-179493800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:179489000-179494200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:179489000-179494400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:179489000-179494800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:179489400-179490600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:179489600-179492000	Enhancers	Brain Cingulate Gyrus	brain
43	chr5:179489800-179490800	Weak transcription	Brain Substantia Nigra	brain
44	chr5:179490000-179491400	Enhancers	Brain Hippocampus Middle	brain
45	chr5:179490200-179491000	Enhancers	HepG2	liver
46	chr5:179490200-179491400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr5:179490200-179492000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:179490400-179491800	Enhancers	Brain Anterior Caudate	brain
49	chr5:179490400-179494000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:179490400-179494000	Weak transcription	Brain Angular Gyrus	brain

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