Variant report

Variant	rs12107948
Chromosome Location	chr3:89748529-89748530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10511146	0.87[AFR][1000 genomes]
rs1104526	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110628	0.87[ASN][1000 genomes]
rs11915277	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11921883	0.87[AFR][1000 genomes]
rs11923274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107534	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12107626	0.87[ASN][1000 genomes]
rs12374054	0.87[ASN][1000 genomes]
rs1589334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027066	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17027069	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17027082	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17027205	0.84[AFR][1000 genomes]
rs1996685	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2049103	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860026	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2881577	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121788	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41404046	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55747951	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55902329	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56035503	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56038553	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56244740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56855556	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56908528	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57036056	0.85[AFR][1000 genomes]
rs57365904	0.83[ASN][1000 genomes]
rs57668063	0.87[ASN][1000 genomes]
rs59194976	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59452230	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59776964	0.87[ASN][1000 genomes]
rs6551423	0.87[AFR][1000 genomes]
rs6771929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775558	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6780506	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6781083	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781208	0.86[AFR][1000 genomes]
rs6781309	0.87[AFR][1000 genomes]
rs6784293	0.87[AFR][1000 genomes]
rs6785223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786215	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6791162	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797049	0.87[ASN][1000 genomes]
rs6804501	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805164	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72912072	0.87[AFR][1000 genomes]
rs72925618	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72925631	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72925647	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72925649	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72929604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929630	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929638	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929663	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616907	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630160	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7630914	0.87[ASN][1000 genomes]
rs7631086	0.93[EUR][1000 genomes]
rs7635408	0.87[ASN][1000 genomes]
rs7635646	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs763900	0.87[ASN][1000 genomes]
rs763901	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1010021	chr3:89521983-90141988	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv530024	chr3:89548440-90304841	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv869889	chr3:89653238-90087372	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1013502	chr3:89670525-89915342	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv536641	chr3:89670525-89915342	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv834761	chr3:89718508-89877335	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89746200-89750600	Enhancers	Duodenum Mucosa	Duodenum
2	chr3:89746400-89748600	Enhancers	Ovary	ovary
3	chr3:89746600-89748800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:89746800-89749400	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr3:89747200-89750200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:89748000-89748600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr3:89748000-89749000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:89748200-89749000	Weak transcription	Colonic Mucosa	Colon

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