Variant report

Variant	rs8025429
Chromosome Location	chr15:78836362-78836363
allele	A/G
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	POLR2A	chr15:78834618-78836610	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78831297..78836398-chr15:78856605..78860226,12	MCF-7	breast:
2	chr15:78832604..78836535-chr15:78856473..78859290,6	MCF-7	breast:

Variant related genes	Relation type
PSMA4	TF binding region
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11630349	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591557	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594391	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900612	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900783	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903129	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906284	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906846	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907169	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907425	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910100	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910726	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910969	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910978	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912022	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12912673	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913173	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915366	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915428	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915652	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1504546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504548	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407257	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847530	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979908	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292117	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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28392948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438420	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2869055	0.91[EUR][1000 genomes]
rs2869544	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743077	0.82[CEU][hapmap]
rs3813571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4275821	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs481134	0.86[CEU][hapmap]
rs4886571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887062	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022780	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555018	0.87[CEU][hapmap]
rs55690619	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56007453	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588765	0.87[CEU][hapmap]
rs601079	0.87[CEU][hapmap]
rs62008174	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62008193	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62008194	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs621849	0.86[CEU][hapmap]
rs647041	0.83[CEU][hapmap]
rs6495306	0.86[CEU][hapmap]
rs6495307	0.83[CEU][hapmap]
rs680244	0.86[CEU][hapmap]
rs7164030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173512	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs8053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905740	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs8025429	CHRNA5	cis	Nerve Tibial	GTEx
rs8025429	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs8025429	RP11-650L12.2	cis	lung	GTEx
rs8025429	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs8025429	CHRNA5	cis	Muscle Skeletal	GTEx
rs8025429	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs8025429	CHRNA3	cis	Muscle Skeletal	GTEx
rs8025429	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs8025429	CHRNA5	cis	lung	GTEx
rs8025429	CHRNA5	cis	Esophagus Mucosa	GTEx
rs8025429	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs8025429	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs8025429	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	chr15:78833600-78838400	Weak transcription	Spleen	Spleen
2	chr15:78833800-78837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:78833800-78838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:78833800-78838000	Weak transcription	Esophagus	oesophagus
5	chr15:78833800-78838000	Weak transcription	Gastric	stomach
6	chr15:78833800-78838400	Weak transcription	Pancreas	Pancrea
7	chr15:78834000-78837600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:78834000-78838000	Weak transcription	Small Intestine	intestine
9	chr15:78834200-78837400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:78834200-78841200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:78834200-78843400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:78834200-78843400	Strong transcription	Placenta	Placenta
13	chr15:78834200-78845000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:78834400-78836800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr15:78834400-78837000	Weak transcription	Brain Anterior Caudate	brain
16	chr15:78834400-78837000	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:78834400-78837000	Weak transcription	Stomach Mucosa	stomach
18	chr15:78834400-78837600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:78834400-78843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:78834400-78843600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:78834400-78843800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:78834400-78843800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:78834600-78836400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr15:78834600-78836800	Weak transcription	Brain Substantia Nigra	brain
25	chr15:78834600-78837000	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr15:78834600-78837200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:78834600-78843200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:78834600-78843600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:78834600-78843800	Strong transcription	Fetal Muscle Leg	muscle
30	chr15:78834800-78836400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr15:78834800-78836400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:78834800-78836400	Genic enhancers	Thymus	Thymus
33	chr15:78834800-78836800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:78834800-78837000	Strong transcription	Fetal Stomach	stomach
35	chr15:78834800-78839600	Strong transcription	Lung	lung
36	chr15:78834800-78842400	Strong transcription	Osteobl	bone
37	chr15:78834800-78843200	Strong transcription	HUVEC	blood vessel
38	chr15:78834800-78843400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:78834800-78843600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr15:78834800-78843600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:78834800-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:78834800-78843600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr15:78834800-78843800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr15:78834800-78843800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:78834800-78843800	Strong transcription	Colon Smooth Muscle	Colon
46	chr15:78834800-78843800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:78834800-78844200	Strong transcription	Fetal Thymus	thymus
48	chr15:78835000-78836800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:78835000-78837200	Weak transcription	NH-A	brain
50	chr15:78835000-78837400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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