Variant report

Variant	rs12902414
Chromosome Location	chr15:76793277-76793278
allele	C/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	chr15:76793264-76793355	MCF-7	breast:	n/a	n/a
2	MYC	chr15:76793264-76793345	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
SCAPER	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11072599	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1125932	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12148786	0.91[ASN][1000 genomes]
rs12148805	0.91[ASN][1000 genomes]
rs12437627	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12438077	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12440815	0.89[AFR][1000 genomes]
rs12441247	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441550	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592171	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592386	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12592420	0.86[ASN][1000 genomes]
rs12593751	0.92[ASN][1000 genomes]
rs12594212	0.91[ASN][1000 genomes]
rs12594577	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12899871	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902174	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903553	0.83[AFR][1000 genomes]
rs12907805	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908421	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12914005	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12915248	0.93[ASN][1000 genomes]
rs12916573	1.00[ASN][1000 genomes]
rs12917430	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1587381	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1588961	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17362383	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17363713	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17364076	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17364330	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17460201	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17461634	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867197	0.89[AFR][1000 genomes]
rs1874944	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875884	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1875885	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1946650	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1965492	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2117369	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2120108	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164101	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2404736	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404737	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs284895	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35077207	0.83[AFR][1000 genomes]
rs35566346	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3866543	0.89[AFR][1000 genomes]
rs4079681	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4633676	0.90[ASN][1000 genomes]
rs4886496	0.80[ASN][1000 genomes]
rs4886799	0.87[ASN][1000 genomes]
rs4886801	0.87[ASN][1000 genomes]
rs4886813	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886817	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56089215	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56216512	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56351018	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57178708	0.89[AFR][1000 genomes]
rs58511211	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58684938	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59088060	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66754747	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66986092	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67204011	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67232575	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67263359	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67418609	0.89[AFR][1000 genomes]
rs67888330	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67920045	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71405216	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7162455	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163946	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7164060	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164813	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165025	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7179142	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7403276	0.86[ASN][1000 genomes]
rs8025134	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030411	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8039545	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8043057	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9646213	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12902414	SCAPER	cis	Artery Tibial	GTEx
rs12902414	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12902414	SCAPER	cis	lung	GTEx
rs12902414	SCAPER	cis	Thyroid	GTEx
rs12902414	SCAPER	cis	Nerve Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76763000-76795000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:76785400-76799800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr15:76788000-76795200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:76788000-76796600	Weak transcription	HSMM	muscle
6	chr15:76788200-76795000	Weak transcription	Primary T cells from cord blood	blood
7	chr15:76788200-76798400	Weak transcription	Dnd41	blood
8	chr15:76788400-76793800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:76788400-76813600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:76789200-76796200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:76789200-76796200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:76789200-76796600	Weak transcription	Adipose Nuclei	Adipose
13	chr15:76789600-76796400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:76790000-76802000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:76790600-76796200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:76791000-76796200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:76791200-76806200	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:76792000-76796400	Enhancers	Fetal Intestine Small	intestine
19	chr15:76792600-76798600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr15:76792600-76801800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:76792800-76794600	Enhancers	Duodenum Mucosa	Duodenum
22	chr15:76793200-76794400	Enhancers	Small Intestine	intestine
23	chr15:76793200-76796400	Enhancers	Fetal Intestine Large	intestine

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