Variant report

Variant	rs28675984
Chromosome Location	chr15:82452471-82452472
allele	A/C
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	STAT3	chr15:82452274-82452764	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr15:82452329-82452851	MCF10A-Er-Src	breast:	n/a	n/a
3	NFIC	chr15:82452089-82452984	SK-N-SH	brain:	n/a	n/a
4	MYC	chr15:82452273-82453035	MCF10A-Er-Src	breast:	n/a	n/a
5	PBX3	chr15:82452151-82452797	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr15:82452121-82452862	SK-N-SH	brain:	n/a	n/a
7	FOS	chr15:82452026-82452829	MCF10A-Er-Src	breast:	n/a	chr15:82452409-82452420
8	STAT3	chr15:82452236-82452696	MCF10A-Er-Src	breast:	n/a	n/a
9	YY1	chr15:82452066-82452748	SK-N-SH	brain:	n/a	n/a
10	YY1	chr15:82452137-82452530	A549	lung:	n/a	n/a
11	JUND	chr15:82452107-82452940	SK-N-SH	brain:	n/a	n/a
12	TAF1	chr15:82452296-82452685	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr15:82452183-82452835	SK-N-SH	brain:	n/a	n/a
14	YY1	chr15:82452145-82452675	SK-N-SH_RA	brain:	n/a	n/a
15	FOSL2	chr15:82452222-82452851	SK-N-SH	brain:	n/a	n/a
16	NFYB	chr15:82452412-82452636	Hela-S3	cervix:	n/a	n/a
17	MAX	chr15:82452104-82452844	SK-N-SH	brain:	n/a	n/a
18	SPI1	chr15:82452463-82452731	GM12891	blood:	n/a	n/a
19	POLR2A	chr15:82452250-82453171	MCF10A-Er-Src	breast:	n/a	n/a
20	SPI1	chr15:82452394-82452645	GM12891	blood:	n/a	n/a
21	EP300	chr15:82452050-82452792	SK-N-SH	brain:	n/a	n/a
22	RXRA	chr15:82452116-82452896	SK-N-SH	brain:	n/a	n/a
23	GATA3	chr15:82452103-82452888	SK-N-SH	brain:	n/a	n/a
24	FOSL2	chr15:82452046-82452851	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr15:82452427-82452560	ProgFib	skin:	n/a	n/a
26	STAT3	chr15:82452291-82452696	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr15:82452127-82452813	SK-N-SH	brain:	n/a	n/a
28	MYC	chr15:82452273-82452879	MCF10A-Er-Src	breast:	n/a	n/a
29	TCF12	chr15:82452030-82452955	SK-N-SH	brain:	n/a	n/a
30	STAT3	chr15:82452378-82452652	MCF10A-Er-Src	breast:	n/a	n/a
31	TEAD4	chr15:82452119-82452897	SK-N-SH	brain:	n/a	n/a
32	FOS	chr15:82452033-82452816	MCF10A-Er-Src	breast:	n/a	chr15:82452409-82452420
33	FOS	chr15:82451802-82452822	HUVEC	blood vessel:	n/a	chr15:82452409-82452420
34	JUND	chr15:82452145-82452806	SK-N-SH	brain:	n/a	n/a
35	NR3C1	chr15:82452204-82452643	A549	lung:	n/a	n/a
36	YY1	chr15:82451950-82452824	SK-N-SH	brain:	n/a	n/a
37	EP300	chr15:82452016-82452889	SK-N-SH	brain:	n/a	n/a
38	FOS	chr15:82452239-82452815	MCF10A-Er-Src	breast:	n/a	chr15:82452409-82452420
39	GATA3	chr15:82452061-82452869	SK-N-SH	brain:	n/a	n/a
40	JUND	chr15:82451898-82452782	SK-N-SH	brain:	n/a	n/a
41	YY1	chr15:82452147-82452612	SK-N-SH_RA	brain:	n/a	n/a
42	TCF12	chr15:82451991-82452946	SK-N-SH	brain:	n/a	n/a
43	FOS	chr15:82451957-82452782	MCF10A-Er-Src	breast:	n/a	chr15:82452409-82452420
44	POLR2A	chr15:82452232-82452842	MCF10A-Er-Src	breast:	n/a	n/a
45	REST	chr15:82452253-82452583	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
EFTUD1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1128431	0.90[ASN][1000 genomes]
rs11852244	0.90[ASN][1000 genomes]
rs11853682	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855145	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856561	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16973420	0.88[ASN][1000 genomes]
rs16973451	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973453	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354842	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292071	0.88[ASN][1000 genomes]
rs28529095	0.87[ASN][1000 genomes]
rs28539162	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28578791	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28754625	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28883606	0.82[ASN][1000 genomes]
rs4725	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4778983	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55914836	0.90[ASN][1000 genomes]
rs56394250	0.84[ASN][1000 genomes]
rs57014042	0.84[ASN][1000 genomes]
rs60855901	0.90[ASN][1000 genomes]
rs61203524	0.87[ASN][1000 genomes]
rs6495644	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66672254	0.88[ASN][1000 genomes]
rs66701409	0.90[ASN][1000 genomes]
rs67988426	0.80[ASN][1000 genomes]
rs71156029	0.88[ASN][1000 genomes]
rs7162177	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73451393	0.86[ASN][1000 genomes]
rs8023960	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032033	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040160	0.86[ASN][1000 genomes]
rs8042665	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920827	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28675984	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs28675984	RP13-608F4.1	cis	Stomach	GTEx
rs28675984	FLJ22795///LOC727751	N/A	lymphoblastoid	RTeQTL
rs28675984	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs28675984	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28675984	RP11-152F13.3	cis	Esophagus Mucosa	GTEx
rs28675984	RP11-152F13.3	cis	lung	GTEx
rs28675984	RP11-152F13.7	cis	Esophagus Mucosa	GTEx
rs28675984	AP3B2	cis	lung	GTEx
rs28675984	AP3B2	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82416400-82454000	Weak transcription	Colonic Mucosa	Colon
2	chr15:82419200-82470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:82420000-82457000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:82420400-82458400	Weak transcription	HepG2	liver
5	chr15:82423200-82454800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:82426000-82457000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:82427600-82456600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:82430400-82455200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:82431200-82455000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:82431200-82461200	Weak transcription	Small Intestine	intestine
11	chr15:82432600-82454800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:82432600-82454800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:82432600-82457800	Weak transcription	Fetal Lung	lung
14	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:82433400-82453800	Weak transcription	Stomach Mucosa	stomach
17	chr15:82433400-82458400	Weak transcription	Fetal Kidney	kidney
18	chr15:82438400-82456800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:82439400-82455400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:82439800-82454800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:82439800-82465600	Weak transcription	K562	blood
22	chr15:82440400-82455000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:82440400-82458200	Weak transcription	HUVEC	blood vessel
24	chr15:82440800-82453000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:82441400-82469600	Weak transcription	Fetal Brain Male	brain
26	chr15:82442800-82454400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:82443000-82453200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:82443000-82454800	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:82443400-82457000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:82444000-82455800	Weak transcription	Fetal Brain Female	brain
31	chr15:82444200-82453600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:82444200-82454400	Weak transcription	Aorta	Aorta
33	chr15:82444200-82454400	Weak transcription	Spleen	Spleen
34	chr15:82444400-82454200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:82444400-82454600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:82444400-82454800	Weak transcription	Brain Angular Gyrus	brain
37	chr15:82444400-82454800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:82444400-82455000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:82444400-82455000	Weak transcription	Right Ventricle	heart
40	chr15:82444400-82465200	Weak transcription	Brain Germinal Matrix	brain
41	chr15:82444600-82453600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:82444600-82454400	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:82444600-82454400	Weak transcription	Fetal Stomach	stomach
44	chr15:82444600-82454400	Weak transcription	Left Ventricle	heart
45	chr15:82444600-82454800	Weak transcription	Brain Anterior Caudate	brain
46	chr15:82444600-82454800	Weak transcription	Brain Substantia Nigra	brain
47	chr15:82444600-82454800	Weak transcription	Ovary	ovary
48	chr15:82444600-82455000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr15:82444600-82455000	Weak transcription	Placenta	Placenta
50	chr15:82444600-82455000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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