Variant report

Variant	rs38152
Chromosome Location	chr7:20047575-20047576
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs38128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38130	0.82[EUR][1000 genomes]
rs38131	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38134	0.82[EUR][1000 genomes]
rs38135	0.82[EUR][1000 genomes]
rs38139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38140	0.82[EUR][1000 genomes]
rs38143	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38144	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38145	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38148	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs38150	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38153	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs38156	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38158	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38160	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62455485	0.94[EUR][1000 genomes]
rs62455486	0.94[EUR][1000 genomes]

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	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1027445	chr7:19947297-20211733	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv887830	chr7:19970584-20114589	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1027849	chr7:20003094-20084998	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2762658	chr7:20023224-20127561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 control	20041166	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:20010200-20052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:20024400-20055400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:20040600-20058800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:20043200-20048800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:20043400-20050400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:20045200-20055200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:20046200-20055400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:20047000-20047600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:20047000-20055600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:20047200-20050400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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