Variant report

Variant	rs6440046
Chromosome Location	chr3:94080813-94080814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11713968	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11714550	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11719701	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12630167	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1492019	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1551423	0.84[AMR][1000 genomes]
rs1979674	0.84[AMR][1000 genomes]
rs1979676	0.83[AMR][1000 genomes]
rs2085143	0.84[AMR][1000 genomes]
rs2087734	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2360106	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28569963	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28636840	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2884903	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36085798	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3912840	0.81[AMR][1000 genomes]
rs4088917	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4104446	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4143023	0.81[AMR][1000 genomes]
rs6440069	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440070	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768190	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6796852	0.81[AMR][1000 genomes]
rs6804969	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806204	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6810367	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7616302	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624232	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7637216	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7644906	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650243	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs768330	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs921725	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9813037	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816169	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816795	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9824571	0.84[AMR][1000 genomes]
rs9826212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835225	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9845562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9851586	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9853108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853331	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9853997	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9855021	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9855371	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9855525	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9856020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9857927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858171	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9858572	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9859818	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9860169	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9863526	0.84[AMR][1000 genomes]
rs9864748	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9865748	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9870513	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9870816	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875906	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9883602	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking 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	23 gene(s)	inside rSNPs	diseases
10	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1000265	chr3:94012384-94259057	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv536650	chr3:94012384-94259057	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv877164	chr3:94018657-94146460	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv877165	chr3:94018657-94160736	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv997698	chr3:94030474-94212738	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv536651	chr3:94030474-94212738	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:94079600-94081200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:94079800-94081200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:94080000-94081400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:94080200-94081200	Weak transcription	Brain Anterior Caudate	brain
5	chr3:94080200-94081200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:94080200-94081400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:94080200-94081400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:94080200-94083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:94080600-94081200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:94080600-94081200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:94080800-94081200	Enhancers	Brain Substantia Nigra	brain

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