Variant report

Variant	rs56197874
Chromosome Location	chr10:5622060-5622061
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs4881481	0.85[ASN][1000 genomes]
rs55794432	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55915230	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019774	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56052209	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56113508	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56172763	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56280752	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56870093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58411480	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58589352	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60208988	0.84[EUR][1000 genomes]
rs61628927	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7898549	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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 target site	68 gene(s)	inside rSNPs	diseases
2	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS 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	24 gene(s)	inside rSNPs	diseases
7	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv894801	chr10:5600202-5631737	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv894802	chr10:5608202-5631737	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv549889	chr10:5610349-5630131	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5617200-5624000	Weak transcription	Colonic Mucosa	Colon
2	chr10:5617400-5623400	Enhancers	HepG2	liver
3	chr10:5617800-5625200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr10:5618800-5624200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:5618800-5625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:5619000-5623800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:5619200-5624000	Weak transcription	Esophagus	oesophagus
8	chr10:5619400-5622600	Weak transcription	Fetal Intestine Small	intestine
9	chr10:5619400-5624000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:5619600-5624000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:5620600-5622800	Enhancers	HMEC	breast
12	chr10:5621000-5622800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:5621400-5622400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:5621600-5624200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:5621800-5625200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:5621800-5625400	Weak transcription	Stomach Mucosa	stomach
17	chr10:5622000-5624600	Weak transcription	Hela-S3	cervix

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dbSNP/dbVar ID: rs12345 /nsv7879
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