Variant report

Variant	rs2568485
Chromosome Location	chr15:78752114-78752115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78591467..78594108-chr15:78749535..78752267,2	K562	blood:
2	chr15:78748240..78750749-chr15:78750932..78754713,4	K562	blood:
3	chr15:78743131..78745408-chr15:78751883..78754148,2	K562	blood:
4	chr15:78743131..78746223-chr15:78751883..78753767,3	K562	blood:
5	chr15:78730050..78732098-chr15:78751945..78754976,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction
ENSG00000140395	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10851906	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072763	0.88[EUR][1000 genomes]
rs11072766	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12101809	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442456	0.84[ASN][1000 genomes]
rs16969894	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036529	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2036533	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568490	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568493	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568497	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2568498	0.88[JPT][hapmap]
rs2568499	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2656055	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2656056	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2656069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656070	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2656071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656072	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656074	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28480606	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28511883	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28602670	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869032	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2869045	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2915695	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2938671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938674	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958719	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35031105	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887053	0.93[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5019044	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs7174190	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174348	0.84[EUR][1000 genomes]
rs924840	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs958025	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9672608	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9788682	0.81[CEU][hapmap]

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	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
2	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
3	esv1806890	chr15:78744695-78786064	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2568485	IREB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
3	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:78739200-78755200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:78739600-78755200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:78740400-78753200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:78740600-78756000	Weak transcription	Brain Germinal Matrix	brain
9	chr15:78741200-78755400	Weak transcription	Fetal Stomach	stomach
10	chr15:78741200-78781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:78742000-78753000	Weak transcription	Dnd41	blood
12	chr15:78742000-78753400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:78742800-78753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:78743000-78752800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:78743200-78755400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:78743200-78755400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:78743200-78756000	Weak transcription	Placenta	Placenta
18	chr15:78743200-78756000	Weak transcription	HMEC	breast
19	chr15:78743200-78759800	Weak transcription	Esophagus	oesophagus
20	chr15:78743800-78754200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:78744600-78755400	Weak transcription	Thymus	Thymus
22	chr15:78746000-78753800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:78746200-78752600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:78746200-78753200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:78746200-78754000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:78746400-78752200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:78747400-78753200	Weak transcription	Primary B cells from cord blood	blood
28	chr15:78747600-78752400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:78747800-78752800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:78748000-78753200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:78748000-78753400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:78748000-78753400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr15:78748000-78753400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:78748000-78753800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:78748400-78753400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:78748400-78756400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:78748600-78752400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:78748600-78753600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:78748600-78756800	Weak transcription	Colonic Mucosa	Colon
40	chr15:78748800-78752400	Weak transcription	K562	blood
41	chr15:78748800-78756000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:78748800-78757000	Weak transcription	Fetal Heart	heart
43	chr15:78749000-78752800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr15:78749000-78753400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:78749000-78753400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:78749000-78753800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:78749000-78755200	Weak transcription	Fetal Thymus	thymus
48	chr15:78749000-78755400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:78749000-78755400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr15:78749000-78755400	Weak transcription	Fetal Muscle Leg	muscle

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