Variant report

Variant	rs28689990
Chromosome Location	chr15:57828002-57828003
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57827683..57829529-chr15:57832472..57835123,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2172606	0.89[AFR][1000 genomes]
rs28393178	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28416157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28609908	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28672256	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28714546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73422836	1.00[AMR][1000 genomes]
rs73422852	1.00[AMR][1000 genomes]
rs73422887	1.00[AMR][1000 genomes]
rs73422892	1.00[AMR][1000 genomes]
rs73422900	1.00[AMR][1000 genomes]
rs73424705	1.00[AMR][1000 genomes]
rs74016316	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:57803200-57842800	Weak transcription	Aorta	Aorta
3	chr15:57819200-57841000	Weak transcription	Esophagus	oesophagus
4	chr15:57819800-57829200	Weak transcription	Ovary	ovary
5	chr15:57819800-57833000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:57819800-57840000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:57820200-57829200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:57820200-57829400	Weak transcription	Brain Angular Gyrus	brain
9	chr15:57820600-57834000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:57821800-57842800	Strong transcription	Liver	Liver
11	chr15:57822400-57829000	Weak transcription	Gastric	stomach
12	chr15:57822600-57829200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:57822800-57833000	Weak transcription	HepG2	liver
14	chr15:57822800-57834000	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:57823000-57828800	Weak transcription	Pancreas	Pancrea
16	chr15:57823600-57828800	Weak transcription	HSMMtube	muscle
17	chr15:57825000-57835800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:57825400-57828600	Weak transcription	Fetal Kidney	kidney
19	chr15:57825400-57831200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:57826000-57834200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:57826200-57829000	Weak transcription	Right Atrium	heart
22	chr15:57826200-57829200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:57826200-57829200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:57826200-57829200	Weak transcription	Brain Substantia Nigra	brain
25	chr15:57826200-57829200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:57826600-57829000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:57826600-57829000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:57826800-57828200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:57826800-57828800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:57826800-57829200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:57826800-57829200	Weak transcription	Fetal Intestine Small	intestine
32	chr15:57827000-57828600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:57827000-57828800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:57827000-57829000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:57827000-57829000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:57827000-57829000	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:57827000-57829200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:57827000-57829600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr15:57827200-57829000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:57827200-57829000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:57827200-57829200	Weak transcription	Adipose Nuclei	Adipose
42	chr15:57827200-57830000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:57827200-57832200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:57827400-57828200	Enhancers	Psoas Muscle	Psoas
45	chr15:57827400-57828600	Weak transcription	NHDF-Ad	bronchial
46	chr15:57827400-57828800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:57827400-57828800	Weak transcription	Left Ventricle	heart
48	chr15:57827400-57829000	Weak transcription	Brain Anterior Caudate	brain
49	chr15:57827400-57829000	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:57827400-57829000	Weak transcription	Right Ventricle	heart

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