Variant report

Variant	rs3743077
Chromosome Location	chr15:78894896-78894897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78892719..78894970-chr15:78895488..78898277,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11637635	0.83[CEU][hapmap]
rs12901300	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902493	0.81[TSI][hapmap]
rs12906951	0.81[TSI][hapmap]
rs12907966	0.83[TSI][hapmap]
rs12910289	0.88[CEU][hapmap]
rs12911602	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12915366	0.81[TSI][hapmap]
rs12916483	0.83[TSI][hapmap]
rs17408276	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1878399	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979906	0.83[TSI][hapmap]
rs1979907	0.82[CEU][hapmap]
rs2067808	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2292117	0.81[TSI][hapmap]
rs2869546	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743073	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs3743074	0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs3743075	0.88[CEU][hapmap];0.89[GIH][hapmap];0.80[EUR][1000 genomes]
rs3743078	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs3813571	0.83[TSI][hapmap]
rs3813572	0.83[TSI][hapmap]
rs472054	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]
rs481134	0.96[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4886571	0.83[TSI][hapmap]
rs495956	0.83[CEU][hapmap]
rs514743	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs518425	0.82[JPT][hapmap]
rs555018	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs578776	0.83[JPT][hapmap]
rs584135	0.88[ASN][1000 genomes]
rs588765	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs601079	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs615470	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62010327	0.84[AMR][1000 genomes]
rs62010328	0.81[AMR][1000 genomes]
rs621849	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs647041	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495306	0.96[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6495307	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs660652	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]
rs680244	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692780	0.83[CEU][hapmap]
rs7182583	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359276	0.81[ASN][1000 genomes]
rs7495518	0.81[AMR][1000 genomes]
rs8025188	0.91[EUR][1000 genomes]
rs8025429	0.82[CEU][hapmap]
rs8053	0.83[TSI][hapmap]
rs952215	0.81[TSI][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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3743077	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs3743077	CHRNA5	cis	Muscle Skeletal	GTEx
rs3743077	CHRNA5	cis	Esophagus Mucosa	GTEx
rs3743077	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs3743077	RP11-650L12.2	cis	lung	GTEx
rs3743077	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs3743077	CHRNA5	cis	lung	GTEx
rs3743077	CHRNA5	cis	Heart Left Ventricle	GTEx
rs3743077	CHRNA5	cis	Nerve Tibial	GTEx
rs3743077	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs3743077	CHRNA5	cis	parietal	SCAN
rs3743077	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs3743077	CHRNA5	cis	cerebellum	SCAN
rs3743077	IREB2	cis	cerebellum	SCAN
rs3743077	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs3743077	PSMA4	cis	cerebellum	SCAN
rs3743077	IREB2	cis	parietal	SCAN
rs3743077	CHRNA3	cis	Muscle Skeletal	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
2	chr15:78880200-78897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:78883000-78896000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:78883000-78896600	Weak transcription	A549	lung
5	chr15:78883400-78897800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:78883800-78895000	Weak transcription	Fetal Intestine Small	intestine
7	chr15:78884400-78901000	Strong transcription	Thymus	Thymus
8	chr15:78884600-78895600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:78884600-78898600	Strong transcription	Fetal Thymus	thymus
10	chr15:78886200-78896400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:78888200-78895400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:78888200-78895800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:78888400-78897200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:78889400-78895800	Weak transcription	Fetal Brain Female	brain
15	chr15:78891600-78896000	Weak transcription	Brain Germinal Matrix	brain
16	chr15:78893200-78895000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr15:78894200-78896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:78894200-78897600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:78894200-78900200	Weak transcription	Fetal Stomach	stomach
20	chr15:78894200-78910600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:78894400-78896200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:78894600-78895200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:78894800-78896200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:78894800-78896800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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