Variant report

Variant	rs2568493
Chromosome Location	chr15:78740233-78740234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78729147..78732824-chr15:78739535..78741823,4	MCF-7	breast:
2	chr15:78728815..78732016-chr15:78740099..78743887,5	MCF-7	breast:
3	chr15:78736823..78739403-chr15:78739443..78741040,2	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	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101809	0.89[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	0.94[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]
rs2568490	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	0.87[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	0.97[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	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656074	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480606	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28511883	0.89[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	0.87[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	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2958719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031105	0.93[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	0.94[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	0.80[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
rs2568493	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	chr15:78732200-78740400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:78732200-78740400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr15:78732200-78741800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:78732200-78742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:78732200-78747600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:78732400-78740600	Strong transcription	Fetal Stomach	stomach
16	chr15:78732400-78740800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:78732400-78742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:78732400-78744400	Weak transcription	Fetal Kidney	kidney
19	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:78733200-78742200	Strong transcription	Fetal Thymus	thymus
21	chr15:78733400-78741000	Weak transcription	Fetal Heart	heart
22	chr15:78733400-78744000	Strong transcription	Primary B cells from cord blood	blood
23	chr15:78733800-78740600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:78733800-78742400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr15:78733800-78743400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:78734000-78742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:78734000-78743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:78734000-78747200	Weak transcription	Fetal Brain Male	brain
29	chr15:78734400-78740400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:78734600-78740600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:78735000-78743600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:78735200-78740400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:78735200-78740600	Strong transcription	Primary T cells from cord blood	blood
34	chr15:78735200-78742000	Strong transcription	Dnd41	blood
35	chr15:78735400-78740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:78735400-78741200	Strong transcription	Thymus	Thymus
37	chr15:78735800-78740400	Strong transcription	Fetal Intestine Large	intestine
38	chr15:78735800-78740600	Strong transcription	HepG2	liver
39	chr15:78735800-78743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:78735800-78744400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:78736400-78740600	Strong transcription	NHLF	lung
42	chr15:78736400-78743000	Strong transcription	Hela-S3	cervix
43	chr15:78736800-78741400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:78736800-78742800	Strong transcription	GM12878-XiMat	blood
45	chr15:78737000-78741000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:78737600-78741200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:78738000-78741200	Strong transcription	HMEC	breast
48	chr15:78738200-78740600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:78738200-78741800	Strong transcription	Colonic Mucosa	Colon
50	chr15:78738400-78740400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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