Variant report

Variant	rs58493575
Chromosome Location	chr5:179341909-179341910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179337210..179339218-chr5:179341502..179344075,2	K562	blood:
2	chr5:179340989..179343245-chr5:179345713..179347574,2	MCF-7	breast:
3	chr5:179333496..179336752-chr5:179337888..179342042,8	K562	blood:
4	chr5:179339541..179342239-chr5:179346452..179348060,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF130-2	chr5:179341389-179342210	NONHSAT105656

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12520005	1.00[AMR][1000 genomes]
rs12521533	1.00[AMR][1000 genomes]
rs17079813	1.00[AMR][1000 genomes]
rs28578757	1.00[AMR][1000 genomes]
rs34823714	1.00[AMR][1000 genomes]
rs58548426	1.00[AMR][1000 genomes]
rs73335521	1.00[AMR][1000 genomes]
rs73338298	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73342216	1.00[AMR][1000 genomes]
rs73344340	1.00[AMR][1000 genomes]
rs73348275	1.00[AMR][1000 genomes]
rs73350175	1.00[AMR][1000 genomes]
rs73810998	1.00[AMR][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	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	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
3	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
4	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179335200-179343000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:179335200-179343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:179335400-179344200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:179335400-179344400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:179335400-179344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:179335400-179346400	Weak transcription	Brain Angular Gyrus	brain
7	chr5:179335400-179346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179335600-179344200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:179336000-179344200	Weak transcription	Primary B cells from cord blood	blood
11	chr5:179336000-179346200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:179336000-179349000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179339400-179342000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:179339400-179342000	Strong transcription	Brain Germinal Matrix	brain
16	chr5:179340400-179342000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:179340800-179342600	Weak transcription	Fetal Brain Male	brain
18	chr5:179340800-179342800	Enhancers	Primary B cells from peripheral blood	blood
19	chr5:179340800-179344400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:179341000-179342600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:179341200-179342000	Strong transcription	Fetal Brain Female	brain
22	chr5:179341400-179343600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:179341400-179344400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:179341600-179342600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:179341600-179343600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:179341600-179343600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:179341600-179344200	Weak transcription	Spleen	Spleen
28	chr5:179341600-179344200	Weak transcription	GM12878-XiMat	blood
29	chr5:179341600-179345800	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:179341600-179346800	Weak transcription	Fetal Thymus	thymus
31	chr5:179341800-179342000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr5:179341800-179342800	Weak transcription	HSMMtube	muscle
33	chr5:179341800-179344200	Weak transcription	Placenta	Placenta

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