Variant report

Variant	rs2568490
Chromosome Location	chr15:78738370-78738371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78735474..78739238-chr15:78747549..78750774,3	MCF-7	breast:
2	chr15:78728296..78733642-chr15:78735614..78739464,6	MCF-7	breast:
3	chr15:78736823..78739403-chr15:78739443..78741040,2	MCF-7	breast:
4	chr15:78729731..78731426-chr15:78738029..78739600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10851906	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072763	0.89[EUR][1000 genomes]
rs11072766	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101809	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12442456	0.81[ASN][1000 genomes]
rs16969894	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036529	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2036533	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568483	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568485	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568488	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568497	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568499	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656055	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656070	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656071	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656072	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480606	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28511883	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28602670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869045	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2915695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938671	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938674	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2958719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031105	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887053	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174190	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174348	0.86[EUR][1000 genomes]
rs924840	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958025	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672608	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2568490	IREB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731400-78745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:78731600-78740600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:78731600-78742800	Weak transcription	Esophagus	oesophagus
4	chr15:78731600-78742800	Weak transcription	Right Ventricle	heart
5	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
7	chr15:78731800-78740400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:78731800-78740800	Weak transcription	Stomach Mucosa	stomach
9	chr15:78732200-78738400	Weak transcription	Brain Substantia Nigra	brain
10	chr15:78732200-78738800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:78732200-78739000	Strong transcription	Placenta	Placenta
12	chr15:78732200-78739600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:78732200-78739800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:78732200-78740400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:78732200-78740400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr15:78732200-78741800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:78732200-78742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:78732200-78747600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:78732400-78739600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:78732400-78740200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:78732400-78740600	Strong transcription	Fetal Stomach	stomach
23	chr15:78732400-78740800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:78732400-78742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:78732400-78744400	Weak transcription	Fetal Kidney	kidney
26	chr15:78732600-78739400	Strong transcription	Osteobl	bone
27	chr15:78732800-78740000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:78733200-78739200	Strong transcription	NH-A	brain
30	chr15:78733200-78742200	Strong transcription	Fetal Thymus	thymus
31	chr15:78733400-78738800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:78733400-78740200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:78733400-78741000	Weak transcription	Fetal Heart	heart
34	chr15:78733400-78744000	Strong transcription	Primary B cells from cord blood	blood
35	chr15:78733600-78739200	Strong transcription	HSMM	muscle
36	chr15:78733800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:78733800-78739200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:78733800-78739200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr15:78733800-78739400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:78733800-78740200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:78733800-78740600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:78733800-78742400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:78733800-78743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:78734000-78739600	Strong transcription	K562	blood
45	chr15:78734000-78740000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:78734000-78740200	Strong transcription	Liver	Liver
47	chr15:78734000-78742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr15:78734000-78743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:78734000-78747200	Weak transcription	Fetal Brain Male	brain
50	chr15:78734200-78740200	Strong transcription	Fetal Muscle Leg	muscle

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