Variant report

Variant	rs10824848
Chromosome Location	chr10:54727219-54727220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10824852	0.89[JPT][hapmap]
rs10824853	0.88[EUR][1000 genomes]
rs10824859	0.94[JPT][hapmap]
rs11003294	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11003295	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11003303	0.94[EUR][1000 genomes]
rs11003341	0.94[JPT][hapmap]
rs11003343	0.94[JPT][hapmap]
rs1343051	0.83[EUR][1000 genomes]
rs1343052	0.88[EUR][1000 genomes]
rs1343070	0.89[EUR][1000 genomes]
rs1539512	0.88[CEU][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs1539513	0.89[JPT][hapmap]
rs1880396	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1917162	0.88[EUR][1000 genomes]
rs1917165	0.90[EUR][1000 genomes]
rs1917166	0.90[EUR][1000 genomes]
rs1917171	0.90[EUR][1000 genomes]
rs1917190	0.94[JPT][hapmap]
rs1949816	0.80[EUR][1000 genomes]
rs2066436	0.88[EUR][1000 genomes]
rs2140671	0.94[EUR][1000 genomes]
rs2244530	0.89[EUR][1000 genomes]
rs2244637	0.89[EUR][1000 genomes]
rs2244778	0.88[EUR][1000 genomes]
rs2462479	0.94[JPT][hapmap]
rs2891425	0.89[JPT][hapmap]
rs4935055	0.94[EUR][1000 genomes]
rs6480983	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7092980	0.94[JPT][hapmap]
rs7095436	0.90[EUR][1000 genomes]
rs7902771	0.84[AMR][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	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	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
3	nsv831877	chr10:54565135-54764638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1041940	chr10:54621342-54737528	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv508584	chr10:54704765-54747382	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10824848	TMOD2	trans	cerebellum	SCAN
rs10824848	RP11-319F12.2	cis	Thyroid	GTEx
rs10824848	ALS2	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54720400-54728000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr10:54724800-54729000	Enhancers	Fetal Intestine Small	intestine
3	chr10:54725000-54730200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr10:54725000-54730400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr10:54725200-54730200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr10:54725200-54730200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr10:54725400-54729800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr10:54725600-54727400	Enhancers	H9 Cell Line	embryonic stem cell
9	chr10:54725600-54730400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr10:54725800-54727400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:54725800-54733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:54726200-54728000	Weak transcription	Fetal Kidney	kidney
13	chr10:54726200-54730000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr10:54726800-54729000	Enhancers	Fetal Intestine Large	intestine
15	chr10:54726800-54729800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr10:54727000-54730000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:54727000-54730000	Enhancers	HepG2	liver
18	chr10:54727200-54727600	Enhancers	GM12878-XiMat	blood

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