Variant report

Variant	rs1917171
Chromosome Location	chr10:54729330-54729331
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10824848	0.90[EUR][1000 genomes]
rs10824853	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11003294	0.92[EUR][1000 genomes]
rs11003295	0.92[EUR][1000 genomes]
rs11003303	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1343051	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1343052	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1343070	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539512	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1880396	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1880397	0.84[ASN][1000 genomes]
rs1917162	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1917165	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1917166	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935936	0.88[ASN][1000 genomes]
rs1949816	0.83[ASN][1000 genomes]
rs2066436	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2140671	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244530	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2244637	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2244778	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2248899	0.84[ASN][1000 genomes]
rs2249349	0.84[ASN][1000 genomes]
rs2249356	0.84[ASN][1000 genomes]
rs2253123	0.84[ASN][1000 genomes]
rs2384100	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2462480	0.84[ASN][1000 genomes]
rs2488606	0.85[ASN][1000 genomes]
rs2492355	0.85[ASN][1000 genomes]
rs4935055	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7095436	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7902771	0.84[ASN][1000 genomes]
rs7906023	0.82[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1917171	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54725000-54730200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr10:54725000-54730400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr10:54725200-54730200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr10:54725200-54730200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr10:54725400-54729800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr10:54725600-54730400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr10:54725800-54733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:54726200-54730000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr10:54726800-54729800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr10:54727000-54730000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:54727000-54730000	Enhancers	HepG2	liver
12	chr10:54727400-54729600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:54727600-54729400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:54728000-54730200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:54729000-54737200	Weak transcription	Fetal Intestine Large	intestine
16	chr10:54729200-54730000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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