Variant report

Variant	rs16973530
Chromosome Location	chr15:75310286-75310287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75307941..75311039-chr15:75492807..75495397,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPCDC-4	chr15:75310211-75310287	NONHSAT047284

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs58954461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59423613	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73432970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438515	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438534	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
3	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
4	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
6	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
8	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
9	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
10	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
15	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
18	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:75304800-75312600	Strong transcription	Brain Anterior Caudate	brain
20	chr15:75304800-75314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:75305000-75315800	Weak transcription	Right Ventricle	heart
22	chr15:75305600-75310800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:75305600-75311400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:75306000-75312400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:75306200-75316000	Weak transcription	Fetal Brain Male	brain
26	chr15:75307600-75310800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:75307800-75315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:75308200-75310400	Strong transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:75308200-75315800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:75308600-75311200	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr15:75308600-75313800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:75308800-75310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:75308800-75312800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr15:75309000-75312600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:75309000-75315800	Weak transcription	Placenta	Placenta
36	chr15:75309200-75310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:75309200-75310800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:75309200-75311400	Strong transcription	Fetal Intestine Large	intestine
39	chr15:75309200-75311600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:75309400-75311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:75309400-75311400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:75309400-75312600	Strong transcription	Gastric	stomach
43	chr15:75309400-75315600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:75309600-75311000	Strong transcription	Pancreas	Pancrea
45	chr15:75309600-75311200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:75309800-75310800	Genic enhancers	Brain Germinal Matrix	brain
47	chr15:75309800-75313600	Strong transcription	Brain Hippocampus Middle	brain
48	chr15:75310000-75311000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr15:75310000-75312000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:75310000-75313600	Strong transcription	Brain Cingulate Gyrus	brain

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