Variant report

Variant	rs28513809
Chromosome Location	chr4:152358543-152358544
allele	C/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:12)

rs_ID	r²[population]
rs10155290	0.81[AMR][1000 genomes]
rs12510777	0.85[AMR][1000 genomes]
rs17027640	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591223	1.00[EUR][1000 genomes]
rs17690873	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28378042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28501688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28505227	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28866051	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4336208	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7685383	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][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	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv432643	chr4:152335395-152417635	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152338400-152362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:152352600-152358800	Weak transcription	Stomach Mucosa	stomach
3	chr4:152354000-152359200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:152354400-152359400	Weak transcription	Pancreas	Pancrea
5	chr4:152354400-152364200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:152354800-152364200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152357600-152358600	Weak transcription	HMEC	breast
8	chr4:152357600-152359600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:152357600-152364200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:152357800-152358600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:152357800-152359000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:152357800-152359000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr4:152357800-152359000	Enhancers	HSMM	muscle
14	chr4:152357800-152359200	Weak transcription	Psoas Muscle	Psoas
15	chr4:152357800-152359400	Enhancers	HSMMtube	muscle
16	chr4:152357800-152359600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:152357800-152362800	Weak transcription	NHEK	skin
18	chr4:152357800-152364200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:152357800-152364200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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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