Variant report

Variant	rs13162328
Chromosome Location	chr5:179496239-179496240
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179490013..179492341-chr5:179495671..179497729,3	MCF-7	breast:
2	chr5:179481868..179484254-chr5:179494865..179496879,2	MCF-7	breast:
3	chr5:179494887..179496936-chr5:179502532..179505071,2	MCF-7	breast:
4	chr5:179494847..179497645-chr5:179497864..179501359,4	K562	blood:
5	chr5:179496103..179499035-chr5:179510851..179514542,4	K562	blood:
6	chr5:179467128..179469131-chr5:179495464..179498336,2	MCF-7	breast:
7	chr5:179452184..179453736-chr5:179495746..179497610,2	MCF-7	breast:
8	chr5:179332913..179335161-chr5:179495987..179497746,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000253480	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10051632	0.96[ASN][1000 genomes]
rs10464097	0.87[AFR][1000 genomes]
rs11249666	0.88[AFR][1000 genomes]
rs13176402	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1540526	0.89[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1947056	0.86[ASN][1000 genomes]
rs2083966	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs3749821	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235506	0.87[ASN][1000 genomes]
rs4290977	0.87[ASN][1000 genomes]
rs4340879	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs4700858	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700859	0.94[AFR][1000 genomes]
rs4700862	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601080	0.87[ASN][1000 genomes]
rs723889	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7706570	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7734329	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7734867	0.99[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13162328	RNF130	cis	brain	BrainEAC

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179476000-179497800	Weak transcription	Lung	lung
3	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
4	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
5	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
6	chr5:179480600-179496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:179481200-179496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:179482600-179496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179484200-179496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:179486800-179496800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179488600-179496800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:179494000-179496400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:179494000-179496600	Enhancers	Fetal Lung	lung
14	chr5:179494000-179497200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:179494200-179496400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:179494200-179496800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:179494200-179496800	Enhancers	Liver	Liver
18	chr5:179494600-179496400	Enhancers	Colon Smooth Muscle	Colon
19	chr5:179494600-179496600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr5:179494800-179496600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:179494800-179497000	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr5:179494800-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:179495000-179496600	Enhancers	Fetal Kidney	kidney
24	chr5:179495000-179496800	Enhancers	A549	lung
25	chr5:179495000-179497800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:179495200-179496400	Weak transcription	Left Ventricle	heart
27	chr5:179495200-179496600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr5:179495200-179496800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:179495200-179496800	Weak transcription	Gastric	stomach
30	chr5:179495200-179498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:179495400-179496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:179495400-179496400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:179495400-179496400	Enhancers	Brain Anterior Caudate	brain
34	chr5:179495400-179496400	Weak transcription	Fetal Stomach	stomach
35	chr5:179495400-179496400	Weak transcription	Pancreas	Pancrea
36	chr5:179495400-179496600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:179495400-179496600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:179495400-179496600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:179495400-179496600	Active TSS	Brain Cingulate Gyrus	brain
40	chr5:179495400-179496600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:179495400-179496600	Enhancers	HepG2	liver
42	chr5:179495400-179496800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:179495400-179496800	Active TSS	Fetal Brain Female	brain
44	chr5:179495400-179499400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:179495600-179496400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:179495600-179496600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:179495600-179496600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:179495600-179497600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr5:179495600-179497800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr5:179495600-179499200	Active TSS	Pancreatic Islets	Pancreatic Islet

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