Variant report

Variant	rs28439064
Chromosome Location	chr15:33246090-33246091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33244808..33246374-chr15:33249318..33251534,2	MCF-7	breast:
2	chr15:33245362..33248334-chr15:33358852..33360940,3	MCF-7	breast:
3	chr15:33244172..33246376-chr15:33247943..33250082,2	K562	blood:
4	chr15:33244592..33247228-chr15:33248722..33251718,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12900473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12900790	1.00[AFR][1000 genomes]
rs12914123	0.91[EUR][1000 genomes]
rs17228999	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17816567	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17816609	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28409161	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28456225	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28463080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28475199	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28475311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485200	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28508587	0.88[EUR][1000 genomes]
rs28544912	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28562592	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28591666	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28661574	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34058116	1.00[AFR][1000 genomes]
rs34176885	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs34953485	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35147427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36097433	1.00[AFR][1000 genomes]
rs67543125	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71462833	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7162402	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8025966	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8029078	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8032279	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8033449	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8033969	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[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	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33232800-33263400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:33234400-33248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:33235000-33248200	Weak transcription	Aorta	Aorta
4	chr15:33238200-33259600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:33243600-33246200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:33243600-33246600	Enhancers	Fetal Stomach	stomach
7	chr15:33243600-33247000	Enhancers	NHDF-Ad	bronchial
8	chr15:33243600-33247800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:33243800-33258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:33243800-33264400	Weak transcription	Gastric	stomach
11	chr15:33244000-33246400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:33244000-33249200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:33244200-33246600	Enhancers	Stomach Smooth Muscle	stomach
14	chr15:33244200-33253800	Weak transcription	Lung	lung
15	chr15:33244400-33246600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:33244400-33247600	Enhancers	Fetal Kidney	kidney
17	chr15:33244600-33246200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:33244800-33246200	Enhancers	Fetal Lung	lung
19	chr15:33244800-33248000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:33245000-33246200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:33245000-33246400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr15:33245000-33246400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr15:33245200-33246200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:33245200-33246400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:33245200-33247000	Enhancers	Fetal Muscle Trunk	muscle
26	chr15:33245200-33248000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:33245200-33274800	Weak transcription	Thymus	Thymus
28	chr15:33245400-33246200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr15:33245600-33246400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:33245600-33248000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:33245600-33259800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr15:33245800-33246200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr15:33245800-33246200	Enhancers	NH-A	brain
34	chr15:33245800-33246800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:33245800-33246800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr15:33245800-33247000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr15:33246000-33246400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr15:33246000-33246400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr15:33246000-33246400	Weak transcription	HSMM	muscle
40	chr15:33246000-33246400	Enhancers	NHLF	lung
41	chr15:33246000-33246600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr15:33246000-33246600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr15:33246000-33246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:33246000-33247000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:33246000-33247200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr15:33246000-33248600	Weak transcription	HSMMtube	muscle
47	chr15:33246000-33248600	Enhancers	Osteobl	bone
48	chr15:33246000-33251200	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:33246000-33251600	Weak transcription	Stomach Mucosa	stomach

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