Variant report

Variant	rs1540526
Chromosome Location	chr5:179511302-179511303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179496103..179499035-chr5:179510851..179514542,4	K562	blood:
2	chr5:179504852..179507239-chr5:179509991..179511932,2	MCF-7	breast:
3	chr5:179497319..179499355-chr5:179510354..179513148,3	MCF-7	breast:
4	chr5:179332164..179334090-chr5:179510604..179512176,2	MCF-7	breast:
5	chr5:179505484..179507567-chr5:179509835..179511460,2	MCF-7	breast:

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:15)

rs_ID	r²[population]
rs10051632	0.84[ASN][1000 genomes]
rs13162328	0.89[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13176402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947056	0.93[ASN][1000 genomes]
rs2083966	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs3749821	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4235506	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4290977	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4340879	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4700858	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4700862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601080	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723889	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7706570	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7734867	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
2	chr5:179508000-179513000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:179508400-179511600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:179508400-179513000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:179508600-179513800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:179508800-179514200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr5:179509000-179513200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179509000-179513200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179509200-179512400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:179509200-179512600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:179509200-179514400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr5:179509400-179512000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:179509400-179517200	Weak transcription	Liver	Liver
14	chr5:179509600-179513400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:179509800-179511600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:179509800-179512800	Enhancers	Brain Germinal Matrix	brain
17	chr5:179510000-179511800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:179510200-179513200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:179510200-179513800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:179510400-179511400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr5:179510400-179512800	Weak transcription	Fetal Brain Male	brain
22	chr5:179510600-179511800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:179510600-179513200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:179510600-179517000	Weak transcription	Fetal Brain Female	brain
25	chr5:179510800-179511400	Weak transcription	K562	blood
26	chr5:179510800-179512000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:179510800-179512200	Weak transcription	Brain Anterior Caudate	brain
28	chr5:179510800-179512600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr5:179510800-179512600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr5:179511000-179512200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:179511000-179514400	Enhancers	Primary hematopoietic stem cells	blood
32	chr5:179511200-179512000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:179511200-179512200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:179511200-179512800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:179511200-179512800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr5:179511200-179513000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:179511200-179513200	Enhancers	Pancreas	Pancrea
38	chr5:179511200-179514000	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links