Variant report

Variant	rs11639224
Chromosome Location	chr15:78753371-78753372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:78753087-78753413	HL-60	blood:	n/a	n/a
2	SPI1	chr15:78753113-78753387	GM12878	blood:	n/a	n/a
3	SPI1	chr15:78753125-78753430	GM12891	blood:	n/a	n/a
4	SPI1	chr15:78753113-78753417	GM12891	blood:	n/a	n/a
5	FOXA1	chr15:78753283-78753740	HepG2	liver:	n/a	n/a
6	FOXA1	chr15:78753356-78753688	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
IREB2	TF binding region
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10519198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072762	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072765	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899131	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910090	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16969899	0.85[LWK][hapmap]
rs1847529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292116	0.88[LWK][hapmap]
rs2568498	1.00[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs2568500	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2656058	0.93[EUR][1000 genomes]
rs2869030	0.85[JPT][hapmap]
rs2869046	0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3743079	0.88[LWK][hapmap]
rs3817092	0.88[LWK][hapmap]
rs4390557	0.89[EUR][1000 genomes]
rs4436747	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8041628	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs954144	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11639224	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs11639224	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs11639224	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs11639224	UBE2Q2	cis	cerebellum	SCAN
rs11639224	IREB2	cis	parietal	SCAN
rs11639224	CHRNA5	cis	parietal	SCAN
rs11639224	CHRNA5	cis	Nerve Tibial	GTEx
rs11639224	IREB2	cis	cerebellum	SCAN
rs11639224	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs11639224	CHRNA5	cis	Muscle Skeletal	GTEx
rs11639224	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs11639224	RP11-650L12.2	cis	lung	GTEx
rs11639224	CHRNA5	cis	cerebellum	SCAN
rs11639224	CHRNA5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 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	chr15:78740600-78756000	Weak transcription	Brain Germinal Matrix	brain
8	chr15:78741200-78755400	Weak transcription	Fetal Stomach	stomach
9	chr15:78741200-78781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:78742000-78753400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:78743200-78755400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:78743200-78755400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:78743200-78756000	Weak transcription	Placenta	Placenta
14	chr15:78743200-78756000	Weak transcription	HMEC	breast
15	chr15:78743200-78759800	Weak transcription	Esophagus	oesophagus
16	chr15:78743800-78754200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:78744600-78755400	Weak transcription	Thymus	Thymus
18	chr15:78746000-78753800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:78746200-78754000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:78748000-78753400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:78748000-78753400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:78748000-78753400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:78748000-78753800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:78748400-78753400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr15:78748400-78756400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:78748600-78753600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:78748600-78756800	Weak transcription	Colonic Mucosa	Colon
28	chr15:78748800-78756000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:78748800-78757000	Weak transcription	Fetal Heart	heart
30	chr15:78749000-78753400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:78749000-78753400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:78749000-78753800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:78749000-78755200	Weak transcription	Fetal Thymus	thymus
34	chr15:78749000-78755400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:78749000-78755400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:78749000-78755400	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:78749000-78755400	Weak transcription	Left Ventricle	heart
38	chr15:78749000-78755400	Weak transcription	Spleen	Spleen
39	chr15:78749000-78756000	Weak transcription	Lung	lung
40	chr15:78749000-78756200	Weak transcription	Fetal Brain Male	brain
41	chr15:78749000-78757000	Weak transcription	Gastric	stomach
42	chr15:78749000-78758600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:78749000-78764800	Weak transcription	Pancreas	Pancrea
44	chr15:78749000-78767800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:78749600-78755400	Weak transcription	HUVEC	blood vessel
46	chr15:78749800-78753600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:78749800-78755400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:78749800-78755400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:78749800-78755400	Weak transcription	Fetal Intestine Small	intestine
50	chr15:78749800-78756000	Weak transcription	NH-A	brain

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