Variant report

Variant	rs647041
Chromosome Location	chr15:78880481-78880482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78878487..78880659-chr15:78887791..78889920,2	MCF-7	breast:
2	chr15:78875573..78878455-chr15:78878955..78880696,2	K562	blood:
3	chr15:78875274..78876810-chr15:78879173..78881083,2	K562	blood:

Variant related genes	Relation type
ENSG00000080644	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11632604	0.80[CEU][hapmap]
rs11636131	0.80[CEU][hapmap]
rs11637635	0.81[CEU][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12901300	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910289	0.88[CEU][hapmap]
rs12911602	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916999	0.80[CEU][hapmap]
rs1504546	0.80[CEU][hapmap]
rs17408276	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1878399	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979905	0.80[CEU][hapmap]
rs1979907	0.83[CEU][hapmap]
rs2067808	0.87[ASN][1000 genomes]
rs2869546	0.88[CEU][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743073	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs3743074	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs3743075	0.88[CEU][hapmap]
rs3743077	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743078	0.80[ASN][1000 genomes]
rs472054	0.88[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481134	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4887064	0.80[CEU][hapmap]
rs495956	0.81[CEU][hapmap]
rs514743	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555018	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs584135	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs588765	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs601079	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs615470	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62010327	0.81[AMR][1000 genomes]
rs621849	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6495306	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6495307	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660652	0.88[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs680244	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs692780	0.81[CEU][hapmap];0.84[AMR][1000 genomes]
rs7164030	0.80[CEU][hapmap]
rs7182583	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7359276	0.82[ASN][1000 genomes]
rs8025188	0.90[EUR][1000 genomes]
rs8025429	0.83[CEU][hapmap]
rs880395	0.80[CEU][hapmap]
rs905740	0.80[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	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
3	nsv518840	chr15:78871288-78887171	Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs647041	RP11-650L12.2	cis	lung	GTEx
rs647041	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs647041	CHRNA5	cis	Nerve Tibial	GTEx
rs647041	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs647041	CHRNA5	cis	Muscle Skeletal	GTEx
rs647041	CHRNA3	cis	Muscle Skeletal	GTEx
rs647041	CHRNA5	cis	Heart Left Ventricle	GTEx
rs647041	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs647041	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs647041	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs647041	CHRNA5	cis	lung	GTEx
rs647041	CHRNA5	cis	Esophagus Mucosa	GTEx
rs647041	RP11-650L12.2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78859200-78882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:78860200-78881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:78860200-78881600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
5	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
6	chr15:78869600-78882000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:78869800-78882200	Weak transcription	A549	lung
8	chr15:78872600-78881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:78873600-78881200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:78877400-78884400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:78877800-78881600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:78877800-78882200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:78877800-78882200	Weak transcription	Thymus	Thymus
14	chr15:78877800-78890400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:78878600-78882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:78878800-78884000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:78879600-78881600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:78880000-78882200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:78880200-78882000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:78880200-78883000	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:78880200-78893400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:78880200-78893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:78880200-78897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:78880400-78882600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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