Variant report

Variant	rs7164848
Chromosome Location	chr15:50663030-50663031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50661266..50664034-chr15:50664188..50666588,3	MCF-7	breast:
2	chr15:50660971..50663378-chr15:50715028..50717755,2	MCF-7	breast:
3	chr15:50661596..50663656-chr15:50716080..50718621,2	MCF-7	breast:
4	chr15:50661068..50663929-chr15:50664392..50666843,2	K562	blood:
5	chr15:50642965..50650579-chr15:50662841..50666750,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50662233-50663533	NONHSAT042412

No data

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1056682	1.00[EUR][1000 genomes]
rs11634585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11857228	0.80[ASN][1000 genomes]
rs11857620	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12902376	0.83[ASN][1000 genomes]
rs12905221	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911017	0.85[EUR][1000 genomes]
rs17431095	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs17431150	1.00[EUR][1000 genomes]
rs17431171	1.00[EUR][1000 genomes]
rs2555486	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs28367473	0.80[ASN][1000 genomes]
rs28489579	0.81[EUR][1000 genomes]
rs28817272	0.90[EUR][1000 genomes]
rs34174311	0.88[EUR][1000 genomes]
rs34565064	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35541701	0.83[EUR][1000 genomes]
rs35628775	0.87[EUR][1000 genomes]
rs35831049	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs4775880	0.89[EUR][1000 genomes]
rs55941574	0.85[EUR][1000 genomes]
rs55948407	0.90[EUR][1000 genomes]
rs606118	1.00[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs66904653	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164431	0.98[ASN][1000 genomes]
rs7167471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs7178670	0.80[ASN][1000 genomes]
rs7182201	1.00[EUR][1000 genomes]
rs720599	1.00[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9673053	0.96[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7164848	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs7164848	TMOD3	cis	parietal	SCAN
rs7164848	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs7164848	GABPB2	cis	uninvolved skin	skin_eQTL
rs7164848	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs7164848	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs7164848	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7164848	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50648200-50664400	Weak transcription	Lung	lung
3	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
4	chr15:50649400-50664000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:50649800-50664200	Weak transcription	Small Intestine	intestine
6	chr15:50649800-50664600	Weak transcription	Psoas Muscle	Psoas
7	chr15:50650000-50663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:50650200-50664000	Weak transcription	Spleen	Spleen
9	chr15:50651400-50664600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:50653000-50664600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:50653200-50666800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:50654200-50664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:50654200-50665000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:50654400-50666400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:50654400-50670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:50654600-50664000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:50654600-50664400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:50654600-50664400	Weak transcription	Fetal Lung	lung
19	chr15:50654600-50664400	Weak transcription	Osteobl	bone
20	chr15:50654600-50664600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:50654600-50666000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:50655200-50663600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:50655200-50664400	Weak transcription	HMEC	breast
24	chr15:50655400-50664600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:50655600-50664600	Weak transcription	Fetal Intestine Large	intestine
26	chr15:50655600-50665200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:50655600-50665400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:50655800-50664200	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:50655800-50666000	Weak transcription	Brain Germinal Matrix	brain
30	chr15:50655800-50666000	Weak transcription	Left Ventricle	heart
31	chr15:50656000-50664400	Weak transcription	Ovary	ovary
32	chr15:50656000-50664800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:50656000-50665800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:50656000-50674200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:50656200-50664400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:50656200-50665000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:50656600-50663200	Weak transcription	Dnd41	blood
38	chr15:50656600-50664400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:50656600-50664600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:50656600-50664600	Weak transcription	Thymus	Thymus
41	chr15:50656600-50664800	Weak transcription	Fetal Thymus	thymus
42	chr15:50657200-50668200	Weak transcription	HSMM	muscle
43	chr15:50657400-50666000	Weak transcription	HSMMtube	muscle
44	chr15:50658200-50664000	Weak transcription	NHEK	skin
45	chr15:50658200-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:50658800-50663200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:50660000-50663200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:50660000-50664800	Strong transcription	Primary T cells from cord blood	blood
49	chr15:50660400-50663200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr15:50660800-50669400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links