Variant report

Variant	rs73407831
Chromosome Location	chr15:55482162-55482163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55478102..55482206-chr15:55486011..55490260,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGB-2	chr15:55482151-55482204	ucscGeneNc_uc002aeh_2

Variant related genes	Relation type
ENSG00000137876	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12324612	1.00[EUR][1000 genomes]
rs28458789	1.00[EUR][1000 genomes]
rs28495958	1.00[EUR][1000 genomes]
rs59104728	1.00[EUR][1000 genomes]
rs60243408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168690	1.00[EUR][1000 genomes]
rs7169189	1.00[EUR][1000 genomes]
rs73407829	1.00[EUR][1000 genomes]
rs73407835	1.00[EUR][1000 genomes]
rs73407844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73409838	1.00[EUR][1000 genomes]
rs73419725	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv525768	chr15:55466155-55485494	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55464800-55488200	Weak transcription	Lung	lung
4	chr15:55466800-55486800	Weak transcription	Psoas Muscle	Psoas
5	chr15:55468800-55487000	Weak transcription	Gastric	stomach
6	chr15:55469200-55484800	Strong transcription	Liver	Liver
7	chr15:55469200-55485000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:55469400-55485200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:55469600-55485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:55469600-55485200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:55469600-55486000	Strong transcription	Primary B cells from cord blood	blood
12	chr15:55469800-55484800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:55469800-55485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:55469800-55486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:55469800-55486600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:55470000-55484800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr15:55470000-55484800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:55470200-55484000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:55470200-55486600	Weak transcription	Small Intestine	intestine
20	chr15:55470400-55485000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:55470400-55485200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:55470400-55486400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:55470400-55486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:55470800-55485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:55471000-55484800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:55471000-55485000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:55471000-55486000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:55471000-55486200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:55471000-55487000	Weak transcription	Pancreas	Pancrea
30	chr15:55471400-55485800	Weak transcription	Stomach Mucosa	stomach
31	chr15:55471600-55486800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:55472000-55484800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:55472000-55485000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:55472000-55486200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:55472200-55488000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:55472400-55488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:55472600-55488400	Weak transcription	Esophagus	oesophagus
38	chr15:55473000-55487000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:55473000-55487400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:55473000-55487600	Weak transcription	Aorta	Aorta
41	chr15:55473600-55486800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:55474200-55486200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:55475000-55487400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:55475200-55484000	Weak transcription	NHLF	lung
45	chr15:55475400-55482800	Weak transcription	Colonic Mucosa	Colon
46	chr15:55475800-55484000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:55476000-55483800	Weak transcription	HSMMtube	muscle
48	chr15:55476400-55483400	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:55476600-55485600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:55477000-55482800	Weak transcription	Brain Angular Gyrus	brain

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