Variant report

Variant	rs472054
Chromosome Location	chr15:78887994-78887995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr15:78887912-78888137	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78882992..78885347-chr15:78887444..78889243,2	K562	blood:
2	chr15:78856606..78859221-chr15:78887185..78889989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261762	TF binding region
ENSG00000169684	Chromatin interaction
ENSG00000261762	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11637635	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12901300	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910289	0.83[CEU][hapmap]
rs12911602	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17408276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878399	0.84[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2067808	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2456019	0.90[AMR][1000 genomes]
rs2869546	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3743073	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3743074	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3743075	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3743077	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3743078	0.84[JPT][hapmap]
rs471889	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs481134	0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs495090	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs495956	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs514743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518425	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs555018	0.83[CEU][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs578776	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs57945453	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs584135	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588765	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs601079	0.84[CEU][hapmap]
rs61012457	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs615470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010327	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62010328	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs621849	0.84[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs647041	0.88[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495306	0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6495307	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs660652	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680244	0.84[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs692780	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7182583	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495518	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8053	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs472054	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs472054	CHRNA5	cis	Muscle Skeletal	GTEx
rs472054	RP11-650L12.2	cis	lung	GTEx
rs472054	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs472054	CHRNA5	cis	lung	GTEx
rs472054	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs472054	CHRNA5	cis	Esophagus Mucosa	GTEx
rs472054	CHRNA5	cis	Nerve Tibial	GTEx
rs472054	CHRNA3	cis	Muscle Skeletal	GTEx
rs472054	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
2	chr15:78877800-78890400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:78880200-78893400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:78880200-78893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:78880200-78897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:78881600-78893200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:78883000-78891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:78883000-78896000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:78883000-78896600	Weak transcription	A549	lung
10	chr15:78883200-78888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:78883200-78889200	Weak transcription	Hela-S3	cervix
12	chr15:78883200-78893600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:78883400-78891400	Weak transcription	Fetal Stomach	stomach
14	chr15:78883400-78897800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:78883600-78893800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:78883800-78895000	Weak transcription	Fetal Intestine Small	intestine
17	chr15:78884200-78893200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:78884400-78901000	Strong transcription	Thymus	Thymus
19	chr15:78884600-78888400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:78884600-78895600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:78884600-78898600	Strong transcription	Fetal Thymus	thymus
22	chr15:78885400-78888200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:78885400-78889000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:78885600-78888200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:78886200-78896400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:78886400-78893800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:78886800-78894000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:78887400-78893600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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