Variant report

Variant	rs10059400
Chromosome Location	chr5:179493833-179493834
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179492115..179494311-chr5:179517115..179518627,2	MCF-7	breast:
2	chr5:179490828..179494547-chr5:179495713..179500418,4	K562	blood:
3	chr5:179466416..179468194-chr5:179492310..179494462,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10051694	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10056316	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10056991	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10066845	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10071652	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10079029	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10464058	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249663	0.87[EUR][1000 genomes]
rs11249664	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11249665	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11249666	0.96[ASN][1000 genomes]
rs11739706	0.87[EUR][1000 genomes]
rs11748441	0.84[EUR][1000 genomes]
rs11750102	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13435998	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17681274	0.87[EUR][1000 genomes]
rs2083967	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34585953	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3776946	0.86[EUR][1000 genomes]
rs3776948	0.86[EUR][1000 genomes]
rs4235505	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4264913	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700852	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700854	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700859	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700864	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57008562	0.86[EUR][1000 genomes]
rs57117216	0.86[EUR][1000 genomes]
rs61356660	0.84[EUR][1000 genomes]
rs62404970	0.86[EUR][1000 genomes]
rs62404974	0.87[EUR][1000 genomes]
rs62404976	0.87[EUR][1000 genomes]
rs62404977	0.87[EUR][1000 genomes]
rs62404979	0.87[EUR][1000 genomes]
rs62405015	0.87[EUR][1000 genomes]
rs6601077	0.86[EUR][1000 genomes]
rs6601078	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6861194	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6862105	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6869349	0.87[EUR][1000 genomes]
rs6873317	0.87[EUR][1000 genomes]
rs6873639	0.87[EUR][1000 genomes]
rs6884565	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7729516	0.87[EUR][1000 genomes]
rs7734329	0.96[ASN][1000 genomes]
rs9329095	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][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:59 , 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	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
9	chr5:179480600-179494000	Weak transcription	Fetal Lung	lung
10	chr5:179480600-179496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:179481200-179496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:179481600-179494600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:179484400-179495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:179484800-179494000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:179486600-179494000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:179486800-179495200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:179486800-179496800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:179487000-179495000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:179487400-179494600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:179487800-179494000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:179488400-179494000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:179488400-179494200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:179488400-179494400	Weak transcription	Fetal Brain Male	brain
26	chr5:179488600-179494000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:179488600-179494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:179488600-179494200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:179488600-179496800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:179488800-179494200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:179489000-179494200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:179489000-179494400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:179489000-179494800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:179490400-179494000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:179490400-179494000	Weak transcription	Brain Angular Gyrus	brain
36	chr5:179490400-179494000	Weak transcription	Fetal Brain Female	brain
37	chr5:179490400-179494800	Weak transcription	NHEK	skin
38	chr5:179491000-179495400	Weak transcription	HepG2	liver
39	chr5:179491400-179494000	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:179491400-179494000	Weak transcription	Brain Substantia Nigra	brain
41	chr5:179491600-179494200	Weak transcription	Liver	Liver
42	chr5:179491600-179494600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:179491800-179494200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:179491800-179494200	Weak transcription	Brain Anterior Caudate	brain
45	chr5:179492000-179494000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:179492000-179494000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:179492200-179494800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:179493200-179494200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:179493200-179494400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:179493600-179494000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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