Variant report

Variant	rs720599
Chromosome Location	chr15:50664515-50664516
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50661266..50664034-chr15:50664188..50666588,3	MCF-7	breast:
2	chr15:50661068..50663929-chr15:50664392..50666843,2	K562	blood:
3	chr15:50642965..50650579-chr15:50662841..50666750,8	K562	blood:
4	chr15:50664439..50666411-chr15:50707371..50708947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1056682	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634585	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12905221	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911017	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17431095	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17431150	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17431171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806843	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2555486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28489579	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28817272	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34174311	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34565064	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35541701	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628775	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35831049	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4775880	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55941574	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55948407	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66904653	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7164848	1.00[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7182201	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs720599	GABPB2	cis	uninvolved skin	skin_eQTL
rs720599	TMOD3	cis	parietal	SCAN
rs720599	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs720599	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs720599	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs720599	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs720599	CTD-3110H11.1	cis	lung	GTEx
rs720599	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs720599	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs720599	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs720599	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs720599	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50649800-50664600	Weak transcription	Psoas Muscle	Psoas
3	chr15:50651400-50664600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:50653000-50664600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:50653200-50666800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:50654200-50665000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:50654400-50666400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:50654400-50670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:50654600-50664600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr15:50654600-50666000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:50655400-50664600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:50655600-50664600	Weak transcription	Fetal Intestine Large	intestine
13	chr15:50655600-50665200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:50655600-50665400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:50655800-50666000	Weak transcription	Brain Germinal Matrix	brain
16	chr15:50655800-50666000	Weak transcription	Left Ventricle	heart
17	chr15:50656000-50664800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:50656000-50665800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:50656000-50674200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:50656200-50665000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:50656600-50664600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:50656600-50664600	Weak transcription	Thymus	Thymus
23	chr15:50656600-50664800	Weak transcription	Fetal Thymus	thymus
24	chr15:50657200-50668200	Weak transcription	HSMM	muscle
25	chr15:50657400-50666000	Weak transcription	HSMMtube	muscle
26	chr15:50658200-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:50660000-50664800	Strong transcription	Primary T cells from cord blood	blood
28	chr15:50660800-50669400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:50661800-50664800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:50662400-50672400	Weak transcription	A549	lung
31	chr15:50663200-50664800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:50663200-50664800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:50663200-50664800	Weak transcription	Fetal Intestine Small	intestine
34	chr15:50663200-50665000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:50663200-50665000	Weak transcription	Fetal Stomach	stomach
36	chr15:50663200-50665600	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:50663200-50670200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:50663400-50669400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:50663400-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:50663600-50669600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:50664400-50664600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:50664400-50664600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:50664400-50664600	Enhancers	Ovary	ovary
44	chr15:50664400-50664800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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