Variant report

Variant	rs12910984
Chromosome Location	chr15:78891627-78891628
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	MAFK	chr15:78891552-78891741	K562	blood:	n/a	chr15:78891668-78891677
2	JUND	chr15:78891602-78891750	K562	blood:	n/a	chr15:78891669-78891678 chr15:78891670-78891679
3	MAFF	chr15:78891602-78891793	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78856903..78859095-chr15:78889415..78893296,3	K562	blood:

Variant related genes	Relation type
CHRNA3	TF binding region
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11637630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593950	0.84[EUR][1000 genomes]
rs13329271	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1700006	0.85[EUR][1000 genomes]
rs2456020	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28534575	0.82[EUR][1000 genomes]
rs28669908	0.85[EUR][1000 genomes]
rs28681284	0.89[EUR][1000 genomes]
rs3743078	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3813570	0.83[TSI][hapmap]
rs3825845	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887069	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs518425	0.84[CEU][hapmap]
rs569207	0.81[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576982	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs578776	0.89[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs637137	0.94[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495308	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6495309	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs667282	0.94[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7170068	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171869	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7177514	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183604	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7359276	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8042059	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042374	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042494	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8043009	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs905739	0.84[AMR][1000 genomes]
rs938682	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12910984	PSMA4	cis	cerebellum	SCAN
rs12910984	COX5A	cis	parietal	SCAN
rs12910984	CHRNA5	cis	Muscle Skeletal	GTEx
rs12910984	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs12910984	CHRNA5	cis	cerebellum	SCAN
rs12910984	PSMA4	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
2	chr15:78880200-78893400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:78880200-78893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78880200-78897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:78881600-78893200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:78883000-78896000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:78883000-78896600	Weak transcription	A549	lung
8	chr15:78883200-78893600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:78883400-78897800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:78883600-78893800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:78883800-78895000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:78884200-78893200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:78884400-78901000	Strong transcription	Thymus	Thymus
14	chr15:78884600-78895600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:78884600-78898600	Strong transcription	Fetal Thymus	thymus
16	chr15:78886200-78896400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:78886400-78893800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:78886800-78894000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:78887400-78893600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:78888200-78895400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:78888200-78895800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:78888400-78897200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:78889400-78895800	Weak transcription	Fetal Brain Female	brain
24	chr15:78891200-78893800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:78891400-78894200	Strong transcription	Fetal Stomach	stomach
26	chr15:78891600-78896000	Weak transcription	Brain Germinal Matrix	brain

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