Variant report

Variant	rs12903050
Chromosome Location	chr15:41836692-41836693
allele	A/T
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	CEBPB	chr15:41836111-41837158	Hela-S3	cervix:	n/a	n/a
2	RFX5	chr15:41836056-41836699	Hela-S3	cervix:	n/a	n/a
3	TAF7	chr15:41836006-41836697	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELF1	chr15:41836049-41836716	GM12878	blood:	n/a	chr15:41836470-41836479
5	GABPA	chr15:41835820-41836692	MCF-7	breast:	n/a	n/a
6	GATA3	chr15:41836310-41836701	T-47D	breast:	n/a	chr15:41836523-41836530 chr15:41836523-41836530 chr15:41836523-41836530
7	POLR2A	chr15:41836188-41836730	GM12891	blood:	n/a	n/a
8	RAD21	chr15:41836369-41836707	SK-N-SH_RA	brain:	n/a	chr15:41836437-41836449
9	YY1	chr15:41835923-41836705	GM12892	blood:	n/a	chr15:41836500-41836511 chr15:41836439-41836447 chr15:41836470-41836479 chr15:41836434-41836443 chr15:41836441-41836449 chr15:41836438-41836460 chr15:41836438-41836448
10	YY1	chr15:41836020-41836715	HepG2	liver:	n/a	chr15:41836500-41836511 chr15:41836439-41836447 chr15:41836470-41836479 chr15:41836434-41836443 chr15:41836441-41836449 chr15:41836438-41836460 chr15:41836438-41836448
11	REST	chr15:41836049-41836719	HL-60	blood:	n/a	chr15:41836570-41836583 chr15:41836575-41836585 chr15:41836567-41836587
12	MAX	chr15:41836074-41837132	NB4	blood:	n/a	n/a
13	POLR2A	chr15:41835908-41836890	K562	blood:	n/a	n/a
14	HEY1	chr15:41836161-41836724	K562	blood:	n/a	chr15:41836582-41836597
15	TAF1	chr15:41835996-41836714	A549	lung:	n/a	n/a
16	POLR2A	chr15:41836045-41836764	Raji	blood:	n/a	n/a
17	STAT5A	chr15:41836100-41836740	K562	blood:	n/a	chr15:41836508-41836520
18	POLR2A	chr15:41836118-41836755	K562	blood:	n/a	n/a
19	REST	chr15:41836150-41836704	H1-neurons	neurons:	n/a	chr15:41836570-41836583 chr15:41836575-41836585 chr15:41836567-41836587
20	POLR2A	chr15:41836235-41836744	GM10847	blood:	n/a	n/a
21	BHLHE40	chr15:41836011-41836700	K562	blood:	n/a	n/a
22	POLR2A	chr15:41836174-41836756	GM19193	blood:	n/a	n/a
23	HCFC1	chr15:41835599-41837113	Hela-S3	cervix:	n/a	n/a
24	GATA1	chr15:41836222-41836717	PBDE	blood:	n/a	chr15:41836523-41836530 chr15:41836523-41836530 chr15:41836523-41836530
25	MAZ	chr15:41836070-41836726	IMR90	lung:	n/a	n/a
26	MYC	chr15:41836205-41837008	NB4	blood:	n/a	n/a
27	CHD2	chr15:41836287-41836703	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:41836045-41836797	MCF-7	breast:	n/a	n/a
29	YY1	chr15:41835932-41836695	GM12878	blood:	n/a	chr15:41836500-41836511 chr15:41836439-41836447 chr15:41836470-41836479 chr15:41836434-41836443 chr15:41836441-41836449 chr15:41836438-41836460 chr15:41836438-41836448
30	POLR2A	chr15:41836187-41836760	GM18505	blood:	n/a	n/a
31	ZNF143	chr15:41836247-41836712	GM12878	blood:	n/a	n/a
32	PML	chr15:41836119-41836707	K562	blood:	n/a	n/a
33	POLR2A	chr15:41836012-41836697	GM12892	blood:	n/a	n/a
34	TAF1	chr15:41835951-41836733	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr15:41835916-41836708	K562	blood:	n/a	n/a
36	ELF1	chr15:41836214-41836720	MCF-7	breast:	n/a	chr15:41836470-41836479
37	POLR2A	chr15:41836067-41836763	HepG2	liver:	n/a	n/a
38	PML	chr15:41835890-41836734	GM12878	blood:	n/a	n/a
39	BCLAF1	chr15:41836235-41836732	GM12878	blood:	n/a	chr15:41836469-41836478 chr15:41836495-41836508 chr15:41836577-41836590
40	POLR2A	chr15:41836165-41836750	Gliobla	brain:	n/a	n/a
41	ELF1	chr15:41836150-41836736	SK-N-SH	brain:	n/a	chr15:41836470-41836479
42	RUNX3	chr15:41836071-41836703	GM12878	blood:	n/a	chr15:41836585-41836600
43	MAX	chr15:41835894-41836717	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr15:41836011-41836791	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr15:41835991-41836885	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr15:41836013-41836728	H1-hESC	embryonic stem cell:	n/a	n/a
47	REST	chr15:41835851-41836966	H1-neurons	neurons:	n/a	chr15:41836570-41836583 chr15:41836575-41836585 chr15:41836567-41836587
48	POLR2A	chr15:41835860-41836811	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr15:41835998-41836929	U87	brain:	n/a	n/a
50	MAX	chr15:41836007-41836716	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62609094..62609648-chr15:41836152..41836752,2	Hela-S3	cervix:
2	chr15:41836247..41836747-chr2:128615430..128615948,2	NB4	blood:
3	chr15:41827251..41831779-chr15:41832424..41837409,12	K562	blood:
4	chr15:41785172..41787151-chr15:41835585..41837884,2	MCF-7	breast:
5	chr15:41834571..41836708-chr15:41849262..41851156,2	K562	blood:
6	chr15:41835713..41840265-chr15:41851401..41853463,4	K562	blood:
7	chr15:41784771..41788118-chr15:41836495..41840463,4	K562	blood:
8	chr15:41836113..41836929-chr9:140135486..140135990,2	HCT-116	colon:
9	chr13:111364110..111365010-chr15:41836304..41837033,2	NB4	blood:
10	chr15:41836411..41836975-chr5:179050328..179051025,2	HCT-116	colon:
11	chr15:41783980..41786928-chr15:41835398..41839034,5	K562	blood:
12	chr15:41784244..41787186-chr15:41835793..41838130,2	MCF-7	breast:
13	chr15:41835700..41837704-chr15:42118864..42120391,2	K562	blood:
14	chr15:41812182..41819156-chr15:41830894..41838104,9	K562	blood:
15	chr15:41407191..41409421-chr15:41835564..41837898,2	MCF-7	breast:
16	chr15:41836090..41836866-chr19:17905832..17906456,2	Hela-S3	cervix:

Variant related genes	Relation type
RPAP1	TF binding region
ENSG00000179913	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000168970	Chromatin interaction
ENSG00000137825	Chromatin interaction
ENSG00000144231	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000250379	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000103932	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11070335	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636126	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855581	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1200352	0.85[ASN][1000 genomes]
rs12442382	0.85[ASN][1000 genomes]
rs12595022	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900977	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906257	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12909551	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012453	0.83[EUR][1000 genomes]
rs2297380	0.81[AMR][1000 genomes]
rs2297381	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28406095	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4420509	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4573907	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167667	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7179280	0.87[ASN][1000 genomes]
rs721772	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028439	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8040440	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040522	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9302110	0.89[ASN][1000 genomes]
rs9744415	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12903050	RPAP1	cis	Esophagus Muscularis	GTEx
rs12903050	RPAP1	cis	Adipose Subcutaneous	GTEx
rs12903050	LTK	cis	lung	GTEx
rs12903050	RPAP1	cis	Artery Tibial	GTEx
rs12903050	TYRO3	cis	lung	GTEx
rs12903050	RPAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41835000-41836800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr15:41835000-41837000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr15:41835000-41837000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:41835200-41836800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:41835200-41836800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr15:41835200-41836800	Active TSS	NHLF	lung
7	chr15:41835200-41837000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:41835400-41836800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr15:41835400-41836800	Active TSS	K562	blood
10	chr15:41835400-41837000	Active TSS	GM12878-XiMat	blood
11	chr15:41835400-41837000	Active TSS	HepG2	liver
12	chr15:41835600-41836800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr15:41835600-41836800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:41835600-41836800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:41835600-41836800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:41835600-41836800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:41835600-41836800	Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:41835600-41836800	Active TSS	Fetal Brain Female	brain
19	chr15:41835600-41836800	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr15:41835600-41836800	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr15:41835600-41836800	Active TSS	NHDF-Ad	bronchial
22	chr15:41835600-41836800	Active TSS	NHEK	skin
23	chr15:41835600-41837000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr15:41835600-41837000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:41835600-41837000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:41835600-41837000	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr15:41835600-41837000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:41835600-41837000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:41835600-41837000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:41835600-41837000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:41835600-41837000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:41835600-41837000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:41835600-41837000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:41835600-41837000	Active TSS	A549	lung
35	chr15:41835600-41837000	Active TSS	HSMM	muscle
36	chr15:41835600-41837000	Active TSS	HSMMtube	muscle
37	chr15:41835800-41836800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr15:41835800-41836800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:41835800-41836800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr15:41835800-41836800	Active TSS	Aorta	Aorta
41	chr15:41835800-41836800	Active TSS	Fetal Kidney	kidney
42	chr15:41835800-41836800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr15:41835800-41836800	Active TSS	Left Ventricle	heart
44	chr15:41835800-41836800	Active TSS	Ovary	ovary
45	chr15:41835800-41836800	Active TSS	Pancreas	Pancrea
46	chr15:41835800-41837000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:41835800-41837000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:41835800-41837000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr15:41835800-41837000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr15:41835800-41837000	Active TSS	Brain Cingulate Gyrus	brain

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