Variant report

Variant	rs28416806
Chromosome Location	chr4:3873144-3873145
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3868448..3872127-chr4:3872488..3876782,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs28435291	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28449795	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28484568	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28489239	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28505188	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28514729	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28521923	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28522536	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28523451	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28525038	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28539438	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28544923	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28553551	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28565417	0.89[ASN][1000 genomes]
rs28612119	0.93[ASN][1000 genomes]
rs28664793	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28689771	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28706592	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34679937	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3979	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58523725	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv878471	chr4:3413209-3884998	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	esv1816543	chr4:3414654-3942867	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1011554	chr4:3436478-3975772	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv537002	chr4:3436478-3975772	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1012371	chr4:3450810-3878976	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv537003	chr4:3450810-3878976	Active TSS Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv998670	chr4:3453787-3909535	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv432549	chr4:3487321-3975048	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv1002558	chr4:3505290-3878976	Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv878508	chr4:3737883-3884998	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv593473	chr4:3792209-3875234	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3872600-3873200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:3872800-3873200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
3	chr4:3872800-3873200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
4	chr4:3872800-3873200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:3872800-3873200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:3872800-3873400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:3872800-3873400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr4:3872800-3873400	Flanking Active TSS	HSMM	muscle
9	chr4:3872800-3873600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
10	chr4:3872800-3873800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:3872800-3873800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:3872800-3874000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr4:3872800-3874200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:3872800-3874200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr4:3872800-3874200	Bivalent Enhancer	Fetal Thymus	thymus
16	chr4:3872800-3874400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:3872800-3874400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:3872800-3875600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr4:3873000-3873200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:3873000-3873200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:3873000-3873200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr4:3873000-3873200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr4:3873000-3873200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:3873000-3873200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr4:3873000-3873200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
26	chr4:3873000-3873200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
27	chr4:3873000-3873400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:3873000-3873400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:3873000-3873400	Bivalent Enhancer	Fetal Brain Male	brain
30	chr4:3873000-3873600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:3873000-3873600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:3873000-3873600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:3873000-3873800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:3873000-3873800	Enhancers	Liver	Liver
35	chr4:3873000-3873800	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr4:3873000-3874000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:3873000-3874000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr4:3873000-3874200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:3873000-3874200	Bivalent Enhancer	Spleen	Spleen
40	chr4:3873000-3874400	Enhancers	Pancreas	Pancrea
41	chr4:3873000-3875600	Active TSS	H9 Cell Line	embryonic stem cell

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