Variant report

Variant	rs2938674
Chromosome Location	chr15:78757913-78757914
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78730612..78732522-chr15:78757828..78760111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10851906	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072763	0.89[EUR][1000 genomes]
rs11072766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101809	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12442456	0.81[ASN][1000 genomes]
rs16969894	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036529	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2036533	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568483	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568485	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]
rs2568488	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568490	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568493	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568497	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568498	0.89[JPT][hapmap];0.81[YRI][hapmap]
rs2568499	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656055	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656056	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2656069	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656070	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2656071	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656072	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2656074	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28480606	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28511883	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28602670	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2869032	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2869045	0.94[CEU][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2915695	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938671	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2958719	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35031105	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887053	0.94[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5019044	1.00[CEU][hapmap]
rs7174190	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174348	0.86[EUR][1000 genomes]
rs924840	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs958025	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9672608	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9788682	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2938674	IREB2	cis	lesional skin	skin_eQTL
rs2938674	IREB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
2	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:78741200-78781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78743200-78759800	Weak transcription	Esophagus	oesophagus
6	chr15:78749000-78758600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:78749000-78764800	Weak transcription	Pancreas	Pancrea
8	chr15:78749000-78767800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:78749800-78764600	Weak transcription	Small Intestine	intestine
10	chr15:78749800-78769600	Weak transcription	Right Ventricle	heart
11	chr15:78750400-78773800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:78751000-78793200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:78752000-78769000	Weak transcription	Psoas Muscle	Psoas
14	chr15:78753000-78760400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:78754000-78789400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:78754200-78760200	Weak transcription	Brain Substantia Nigra	brain
17	chr15:78754400-78758600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:78754400-78760200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:78754400-78760600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:78754400-78787600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:78754600-78771200	Strong transcription	HepG2	liver
22	chr15:78754600-78773600	Strong transcription	A549	lung
23	chr15:78754600-78793400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:78754800-78771600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:78754800-78793800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr15:78755000-78758600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:78755000-78758600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:78755000-78762600	Strong transcription	Dnd41	blood
29	chr15:78755000-78772800	Strong transcription	Hela-S3	cervix
30	chr15:78755000-78787000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:78755000-78787000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:78755000-78793800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:78755000-78794400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr15:78755200-78758800	Strong transcription	HSMMtube	muscle
35	chr15:78755200-78759400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:78755200-78761000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr15:78755200-78761000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr15:78755200-78761400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:78755200-78761400	Strong transcription	Fetal Intestine Large	intestine
40	chr15:78755200-78772200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr15:78755200-78772600	Strong transcription	Primary B cells from cord blood	blood
42	chr15:78755200-78772600	Strong transcription	Osteobl	bone
43	chr15:78755200-78772800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:78755200-78773800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:78755200-78779000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:78755200-78783800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr15:78755200-78787000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:78755200-78792600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:78755200-78793400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:78755200-78793600	Strong transcription	Rectal Mucosa Donor 29	rectum

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