Variant report

Variant	rs12644228
Chromosome Location	chr4:124506557-124506558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12643847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644121	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644620	1.00[ASN][1000 genomes]
rs12646555	1.00[ASN][1000 genomes]
rs17007024	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17007051	0.93[ASN][1000 genomes]
rs28827850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57111794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57235450	0.96[ASN][1000 genomes]
rs57904792	0.89[ASN][1000 genomes]
rs57940178	0.93[ASN][1000 genomes]
rs58280008	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58535348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59621223	0.89[ASN][1000 genomes]
rs59791195	1.00[ASN][1000 genomes]
rs60096196	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60289595	1.00[ASN][1000 genomes]
rs60795072	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6534417	1.00[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	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv879871	chr4:124437842-124527958	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv879872	chr4:124441989-124527958	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv469710	chr4:124474286-124623722	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv482747	chr4:124474286-124623722	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124503200-124508600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:124503400-124509400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:124503800-124509400	Weak transcription	Right Atrium	heart
4	chr4:124504000-124509200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:124504400-124509200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:124504400-124509200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:124504400-124509400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:124504600-124509200	Weak transcription	NHEK	skin
9	chr4:124505000-124508600	Weak transcription	HMEC	breast
10	chr4:124505200-124508800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:124505600-124506600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:124506200-124506600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr4:124506200-124506600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:124506400-124509200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:124506400-124519600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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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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