Variant report

Variant	rs55966152
Chromosome Location	chr15:58561006-58561007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1123294	0.85[EUR][1000 genomes]
rs55760919	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62001667	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62001668	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62001669	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62001677	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7165301	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8040386	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1050473	chr15:58479888-58562270	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv904264	chr15:58505122-58588510	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv904265	chr15:58517528-58588510	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58550400-58561800	Weak transcription	Liver	Liver
2	chr15:58553200-58562200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:58553400-58562400	Weak transcription	Spleen	Spleen
4	chr15:58554200-58574400	Weak transcription	Left Ventricle	heart
5	chr15:58557400-58561400	Weak transcription	Primary T cells from cord blood	blood
6	chr15:58557400-58562400	Weak transcription	Dnd41	blood
7	chr15:58558800-58562200	Enhancers	NHEK	skin
8	chr15:58559000-58562400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:58559000-58562600	Enhancers	Hela-S3	cervix
10	chr15:58559200-58562200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:58559200-58562800	Enhancers	Placenta	Placenta
12	chr15:58559600-58561400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr15:58559800-58561200	Weak transcription	HMEC	breast
14	chr15:58559800-58562400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:58560400-58562800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:58560600-58562600	Enhancers	Thymus	Thymus
17	chr15:58561000-58562600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:58561000-58562600	Enhancers	GM12878-XiMat	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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