Variant report

Variant	rs7717213
Chromosome Location	chr5:179346466-179346467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179344667..179348658-chr5:179348694..179351891,3	MCF-7	breast:
2	chr5:179334067..179337009-chr5:179345090..179348223,4	MCF-7	breast:
3	chr5:179340989..179343245-chr5:179345713..179347574,2	MCF-7	breast:
4	chr5:179339541..179342239-chr5:179346452..179348060,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF130-1	chr5:179345911-179347229	NONHSAT105657

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10078686	1.00[MEX][hapmap]
rs17079679	1.00[MEX][hapmap]
rs269459	1.00[MEX][hapmap]
rs269469	1.00[TSI][hapmap]
rs272440	1.00[MEX][hapmap]
rs407437	1.00[TSI][hapmap]
rs73338301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73340208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73340210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9687148	1.00[EUR][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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179335400-179346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:179336000-179349000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:179341600-179346800	Weak transcription	Fetal Thymus	thymus
6	chr5:179343000-179348000	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:179344200-179347400	Strong transcription	Brain Germinal Matrix	brain
8	chr5:179344400-179347000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:179344600-179347600	Strong transcription	Fetal Brain Female	brain
10	chr5:179344600-179381600	Weak transcription	Fetal Brain Male	brain
11	chr5:179344800-179346600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:179344800-179346600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:179344800-179350400	Weak transcription	Primary B cells from cord blood	blood
14	chr5:179344800-179350400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr5:179344800-179351400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:179345000-179347000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:179345000-179350200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr5:179345000-179350400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:179345400-179347200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:179345800-179347400	Strong transcription	Brain Hippocampus Middle	brain
21	chr5:179346200-179346800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:179346200-179347000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:179346400-179346600	Enhancers	Spleen	Spleen
24	chr5:179346400-179347000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr5:179346400-179347200	Strong transcription	Brain Angular Gyrus	brain
26	chr5:179346400-179347200	Strong transcription	Fetal Stomach	stomach

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