Variant report

Variant	rs7250868
Chromosome Location	chr19:38358810-38358811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10401637	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10401968	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10402530	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10404567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs10409402	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10409487	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10415548	0.80[CEU][hapmap]
rs10420746	1.00[CEU][hapmap]
rs10420891	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10427125	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083432	1.00[CEU][hapmap]
rs1119229	0.85[CEU][hapmap]
rs11878269	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11879180	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1291	1.00[CEU][hapmap]
rs12974225	1.00[CEU][hapmap]
rs12975057	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12979640	1.00[CEU][hapmap]
rs1643466	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs1643467	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1643468	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1725481	1.00[CEU][hapmap]
rs1725482	1.00[CEU][hapmap]
rs1725499	0.80[CEU][hapmap]
rs2068431	0.81[ASN][1000 genomes]
rs2075281	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287229	1.00[CEU][hapmap]
rs241932	1.00[CEU][hapmap]
rs2909093	0.92[CEU][hapmap]
rs2909098	1.00[CEU][hapmap]
rs2909102	1.00[CEU][hapmap]
rs2909105	1.00[CEU][hapmap]
rs2927747	1.00[CEU][hapmap]
rs2972437	1.00[CEU][hapmap]
rs2972438	1.00[CEU][hapmap]
rs2972439	1.00[CEU][hapmap]
rs3095726	1.00[CEU][hapmap]
rs35209753	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs353410	0.80[CEU][hapmap]
rs353411	0.80[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs353415	1.00[CEU][hapmap]
rs353423	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap]
rs3848626	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802135	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803509	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4803524	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803528	0.81[ASN][1000 genomes]
rs4803551	0.85[CEU][hapmap]
rs4803573	0.85[CEU][hapmap]
rs58449039	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508742	0.83[EUR][1000 genomes]
rs705491	0.85[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs705493	0.85[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs705495	0.85[CEU][hapmap]
rs7250409	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7250571	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252010	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257125	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7258597	0.86[EUR][1000 genomes]
rs8101752	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8101858	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104076	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs8112706	1.00[CEU][hapmap]
rs8113521	0.80[CEU][hapmap]
rs8182498	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs833895	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs833914	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs833926	1.00[CEU][hapmap]
rs856300	0.92[CEU][hapmap]
rs856304	1.00[CEU][hapmap]
rs9304569	0.83[EUR][1000 genomes]
rs9304572	0.84[EUR][1000 genomes]
rs958305	1.00[CEU][hapmap]
rs968073	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1832898	chr19:38341754-38362792	Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1825275	chr19:38341754-38376485	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv960836	chr19:38355208-38370306	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7250868	ZNF571	cis	multi-tissue	Pritchard
rs7250868	WDR87	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38355200-38359000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr19:38356200-38365600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:38356800-38365600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:38357800-38359200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr19:38357800-38359200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:38358000-38359000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:38358200-38359000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:38358200-38359200	Enhancers	NHEK	skin
9	chr19:38358400-38359000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:38358600-38359200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell

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