Variant report

Variant	rs10279431
Chromosome Location	chr7:48153838-48153839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10225490	0.82[EUR][1000 genomes]
rs10263327	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274287	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10278827	0.81[EUR][1000 genomes]
rs6463463	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463464	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6945143	0.87[EUR][1000 genomes]
rs6962799	0.85[EUR][1000 genomes]
rs7455481	0.85[EUR][1000 genomes]
rs7784208	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639995	0.87[EUR][1000 genomes]
rs9648572	0.93[AMR][1000 genomes];0.95[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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1033738	chr7:48143988-48349357	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10279431	UPP1	cis	cerebellum	SCAN
rs10279431	PKD1L1	cis	cerebellum	SCAN
rs10279431	PKD1L1	cis	parietal	SCAN
rs10279431	C7orf72	cis	cerebellum	SCAN
rs10279431	YKT6	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48138800-48156200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:48143000-48156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:48148000-48155800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:48148600-48154200	Weak transcription	Aorta	Aorta
5	chr7:48148600-48158200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:48149000-48155800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:48149200-48154000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:48149400-48154000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:48149400-48156200	Weak transcription	Spleen	Spleen
10	chr7:48149600-48155800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:48150400-48154000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:48151400-48154400	Enhancers	NHEK	skin
13	chr7:48151800-48154600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:48151800-48154600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:48151800-48154800	Enhancers	HMEC	breast
16	chr7:48151800-48155400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:48152200-48154000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:48153200-48154600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:48153600-48154000	Bivalent Enhancer	HepG2	liver
20	chr7:48153600-48154600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:48153600-48154600	Enhancers	Esophagus	oesophagus
22	chr7:48153600-48154600	Enhancers	Placenta	Placenta
23	chr7:48153800-48154000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:48153800-48154000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:48153800-48154200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links