Variant report

Variant	rs3816974
Chromosome Location	chr5:53258698-53258699
allele	A/T
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:10)

rs_ID	r²[population]
rs13187145	0.87[ASN][1000 genomes]
rs16881847	0.81[ASN][1000 genomes]
rs16881895	0.90[ASN][1000 genomes]
rs1838724	0.88[ASN][1000 genomes]
rs56016819	0.90[ASN][1000 genomes]
rs58614496	0.86[ASN][1000 genomes]
rs66505436	0.90[ASN][1000 genomes]
rs68101674	0.90[ASN][1000 genomes]
rs713209	0.84[ASN][1000 genomes]
rs7726524	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv880272	chr5:53213945-53277266	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 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	chr5:53239000-53271000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:53243600-53258800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:53253000-53265200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:53253600-53294800	Weak transcription	Primary B cells from cord blood	blood
5	chr5:53255600-53261400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:53255600-53264200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:53255600-53265800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:53255600-53268400	Weak transcription	Aorta	Aorta
9	chr5:53255600-53286200	Weak transcription	Fetal Intestine Large	intestine
10	chr5:53255800-53270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:53256800-53310000	Weak transcription	Primary T cells from cord blood	blood
12	chr5:53257600-53259200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:53257800-53259200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:53257800-53259400	Enhancers	NHDF-Ad	bronchial
15	chr5:53258000-53274000	Weak transcription	K562	blood
16	chr5:53258400-53260600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:53258400-53266600	Weak transcription	Rectal Smooth Muscle	rectum

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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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