Variant report

Variant	rs28461632
Chromosome Location	chr15:30107483-30107484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:30095523..30098044-chr15:30106073..30108934,2	MCF-7	breast:
2	chr15:30104918..30110272-chr15:30111258..30116596,7	MCF-7	breast:
3	chr15:30103514..30110154-chr15:30110674..30116017,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction
ENSG00000259523	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16954392	0.91[AFR][1000 genomes]
rs16955734	1.00[LWK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs2293185	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs28729338	0.91[AFR][1000 genomes]
rs36012099	0.86[AFR][1000 genomes]
rs45456792	1.00[AFR][1000 genomes]
rs45611333	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv1845759	chr15:30097078-30142373	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
2	chr15:30082400-30113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:30086000-30107600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:30091800-30108000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:30092600-30111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:30093000-30107600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:30094600-30107600	Weak transcription	Left Ventricle	heart
8	chr15:30097800-30107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:30098000-30107600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:30098000-30111600	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:30098000-30112400	Weak transcription	Fetal Stomach	stomach
12	chr15:30098200-30107600	Weak transcription	Ovary	ovary
13	chr15:30098400-30111600	Weak transcription	HSMMtube	muscle
14	chr15:30099000-30107600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:30100800-30108200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:30102400-30108600	Enhancers	Brain Anterior Caudate	brain
17	chr15:30102600-30108800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr15:30102600-30108800	Enhancers	Brain Hippocampus Middle	brain
19	chr15:30102800-30108800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr15:30103000-30108200	Weak transcription	Aorta	Aorta
21	chr15:30103000-30108200	Weak transcription	Psoas Muscle	Psoas
22	chr15:30103000-30108400	Enhancers	Brain Substantia Nigra	brain
23	chr15:30103200-30107600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:30103800-30109000	Enhancers	NHDF-Ad	bronchial
25	chr15:30104000-30109000	Enhancers	Fetal Heart	heart
26	chr15:30104200-30108400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:30104200-30108600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:30104400-30107600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:30104400-30107800	Weak transcription	Fetal Kidney	kidney
30	chr15:30104600-30108200	Weak transcription	Placenta	Placenta
31	chr15:30104600-30108600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:30104800-30108000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:30104800-30108200	Enhancers	NHLF	lung
34	chr15:30104800-30108800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:30105200-30111800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:30105400-30108000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:30105600-30108600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:30105600-30109000	Enhancers	Liver	Liver
39	chr15:30105600-30112000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:30105800-30108400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr15:30106000-30107600	Weak transcription	Fetal Lung	lung
42	chr15:30106000-30107800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:30106000-30108000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:30106000-30109000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr15:30106200-30108000	Weak transcription	NH-A	brain
46	chr15:30106200-30108400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr15:30106200-30108400	Weak transcription	Right Atrium	heart
48	chr15:30106200-30112000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:30106200-30112200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:30106400-30108000	Weak transcription	Rectal Smooth Muscle	rectum

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