Variant report

Variant	rs17022451
Chromosome Location	chr4:95804014-95804015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11932204	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11932515	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11932610	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935769	0.85[YRI][hapmap]
rs11936523	0.92[EUR][1000 genomes]
rs11941775	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11943147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1541368	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1541370	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1541371	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022139	0.83[YRI][hapmap]
rs17022361	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022438	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022440	1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17022443	1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17022456	0.92[EUR][1000 genomes]
rs17022474	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022484	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17022491	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022496	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17022509	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022514	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022528	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022567	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2865408	1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56353739	0.92[EUR][1000 genomes]
rs57560594	0.92[EUR][1000 genomes]
rs58414599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58554231	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61352548	0.81[AFR][1000 genomes]
rs6828737	0.92[EUR][1000 genomes]
rs6829384	0.92[EUR][1000 genomes]
rs6851515	0.92[EUR][1000 genomes]
rs6851550	0.92[EUR][1000 genomes]
rs6851705	0.92[EUR][1000 genomes]
rs72887844	0.92[EUR][1000 genomes]
rs72887846	0.92[EUR][1000 genomes]
rs73836127	0.92[EUR][1000 genomes]
rs73836128	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73836142	1.00[EUR][1000 genomes]
rs73836153	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73836154	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73836181	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73836183	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73836186	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73836191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7669132	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7669913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17022451	SCGB1D2	trans	brain	seeQTL
rs17022451	SCGB2A2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95781200-95810600	Weak transcription	Fetal Kidney	kidney
2	chr4:95793400-95810600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:95800000-95810600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:95802600-95805400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:95803200-95806000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:95804000-95804400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:95804000-95804600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:95804000-95813200	Weak transcription	A549	lung

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