Variant report

Variant	rs1949816
Chromosome Location	chr10:54767286-54767287
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10824848	0.80[EUR][1000 genomes]
rs10824853	0.88[ASN][1000 genomes]
rs11003303	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1343051	0.86[ASN][1000 genomes]
rs1343052	0.88[ASN][1000 genomes]
rs1343070	0.89[ASN][1000 genomes]
rs1539512	0.87[ASN][1000 genomes]
rs1880397	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1917162	0.88[ASN][1000 genomes]
rs1917165	0.85[ASN][1000 genomes]
rs1917166	0.85[ASN][1000 genomes]
rs1917171	0.83[ASN][1000 genomes]
rs1935936	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066436	0.93[ASN][1000 genomes]
rs2140671	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2244530	0.95[ASN][1000 genomes]
rs2244637	0.95[ASN][1000 genomes]
rs2244778	0.93[ASN][1000 genomes]
rs2248899	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249349	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249356	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253123	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462480	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488606	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492355	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4935055	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7095436	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv1826571	chr10:54765608-54788821	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv895405	chr10:54765608-54824741	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1949816	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54764400-54771200	Enhancers	HepG2	liver
2	chr10:54764800-54767600	Enhancers	Liver	Liver
3	chr10:54765200-54782600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:54765600-54767600	Enhancers	Fetal Intestine Small	intestine
5	chr10:54765600-54767600	Enhancers	Fetal Kidney	kidney
6	chr10:54765800-54767600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr10:54766000-54767600	Enhancers	Fetal Intestine Large	intestine
8	chr10:54766200-54767600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:54766400-54767600	Enhancers	Duodenum Mucosa	Duodenum
10	chr10:54766600-54767600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr10:54766800-54767600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:54766800-54770000	Weak transcription	Stomach Mucosa	stomach
13	chr10:54767200-54767400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr10:54767200-54767400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr10:54767200-54767600	Enhancers	Fetal Lung	lung

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