Variant report

Variant	rs2555486
Chromosome Location	chr15:50656121-50656122
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50651977-50656135	K562	blood:	n/a	n/a
2	POLR2A	chr15:50652123-50656758	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr15:50655848-50656138	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr15:50655882-50656136	HepG2	liver:	n/a	n/a
6	FOXA1	chr15:50655819-50656151	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50655847..50659285-chr15:50680641..50684000,3	MCF-7	breast:
2	chr15:50654014..50656203-chr15:50714863..50719215,3	K562	blood:
3	chr15:50654234..50656265-chr15:50779906..50781623,2	MCF-7	breast:
4	chr15:50653739..50656300-chr15:50709465..50712188,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50655802-50656641	NONHSAT042412
2	lnc-USP8-2	chr15:50655998-50658705	ENSG00000246338

No data

Variant related genes	Relation type
ENSG00000259715	TF binding region
ENSG00000138592	Chromatin interaction
ENSG00000259465	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1056682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634585	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12905221	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12911017	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17431095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17431150	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17431171	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806843	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs28489579	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28817272	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34174311	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34565064	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35541701	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628775	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35831049	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4775880	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55941574	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55948407	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66904653	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7164848	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7182201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720599	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]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2555486	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs2555486	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs2555486	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs2555486	GABPB2	cis	uninvolved skin	skin_eQTL
rs2555486	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2555486	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs2555486	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs2555486	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2555486	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs2555486	CTD-3110H11.1	cis	lung	GTEx
rs2555486	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50648200-50657200	Weak transcription	Esophagus	oesophagus
3	chr15:50648200-50658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:50648200-50664400	Weak transcription	Lung	lung
5	chr15:50648400-50660400	Weak transcription	Aorta	Aorta
6	chr15:50649000-50658600	Weak transcription	Right Atrium	heart
7	chr15:50649200-50656400	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
9	chr15:50649400-50656600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:50649400-50657800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:50649400-50659200	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:50649400-50664000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:50649600-50656600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:50649600-50656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:50649600-50657400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:50649600-50660600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:50649600-50661800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:50649800-50656600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:50649800-50664200	Weak transcription	Small Intestine	intestine
20	chr15:50649800-50664600	Weak transcription	Psoas Muscle	Psoas
21	chr15:50650000-50656400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:50650000-50658000	Weak transcription	Fetal Heart	heart
23	chr15:50650000-50663000	Weak transcription	Fetal Brain Male	brain
24	chr15:50650000-50663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:50650200-50658200	Strong transcription	NHEK	skin
26	chr15:50650200-50662600	Weak transcription	NH-A	brain
27	chr15:50650200-50664000	Weak transcription	Spleen	Spleen
28	chr15:50650800-50659400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:50651200-50656600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:50651400-50656200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:50651400-50656600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:50651400-50658800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:50651400-50659200	Strong transcription	A549	lung
34	chr15:50651400-50660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:50651400-50660800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:50651400-50661600	Weak transcription	NHDF-Ad	bronchial
37	chr15:50651400-50664600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:50652000-50656600	Strong transcription	Dnd41	blood
39	chr15:50652000-50657400	Strong transcription	HSMMtube	muscle
40	chr15:50652200-50656600	Strong transcription	Fetal Thymus	thymus
41	chr15:50652400-50656200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr15:50653000-50662600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:50653000-50664600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:50653200-50660200	Weak transcription	Fetal Stomach	stomach
45	chr15:50653200-50662800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:50653200-50666800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:50653400-50662600	Weak transcription	Fetal Intestine Small	intestine
48	chr15:50653600-50656200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:50653800-50656200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:50653800-50656600	Strong transcription	Thymus	Thymus

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