Variant report

Variant	rs504781
Chromosome Location	chr15:50648339-50648340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:40)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr15:50646984-50648470	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:50648225-50648460	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:50645890-50649461	GM18505	blood:	n/a	n/a
4	POLR2A	chr15:50643941-50650733	GM12891	blood:	n/a	n/a
5	SIN3AK20	chr15:50645321-50648400	MCF-7	breast:	n/a	n/a
6	POLR2A	chr15:50645476-50650223	GM12878	blood:	n/a	n/a
7	MYC	chr15:50646867-50648401	K562	blood:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
8	MAX	chr15:50645921-50648376	A549	lung:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
9	TBP	chr15:50646936-50648530	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:50646743-50648506	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr15:50646827-50649588	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:50645817-50648434	GM18526	blood:	n/a	n/a
13	POLR2A	chr15:50645950-50649548	K562	blood:	n/a	n/a
14	MTA3	chr15:50645838-50649091	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:50643964-50649543	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:50645530-50650223	K562	blood:	n/a	n/a
17	POLR2A	chr15:50646823-50648645	HCT-116	colon:	n/a	n/a
18	POLR2A	chr15:50645340-50648555	HUVEC	blood vessel:	n/a	n/a
19	IRF1	chr15:50646762-50648678	K562	blood:	n/a	chr15:50647099-50647108
20	POLR2A	chr15:50645943-50648494	GM12892	blood:	n/a	n/a
21	POLR2A	chr15:50645808-50650538	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:50645990-50648485	Raji	blood:	n/a	n/a
23	NRF1	chr15:50646352-50648412	SK-N-SH	brain:	n/a	chr15:50647650-50647661 chr15:50647647-50647661 chr15:50647650-50647661 chr15:50647652-50647661 chr15:50647371-50647380
24	POLR2A	chr15:50648250-50648495	Hela-S3	cervix:	n/a	n/a
25	GTF2F1	chr15:50646976-50648361	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr15:50646010-50648501	GM15510	blood:	n/a	n/a
27	POLR2A	chr15:50645486-50648569	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:50645780-50648825	GM12892	blood:	n/a	n/a
29	MXI1	chr15:50646900-50648462	Hela-S3	cervix:	n/a	n/a
30	BCL3	chr15:50646855-50648452	A549	lung:	n/a	chr15:50646876-50646889 chr15:50646909-50646918 chr15:50647100-50647109
31	SIN3AK20	chr15:50645301-50648579	MCF-7	breast:	n/a	n/a
32	POLR2A	chr15:50648293-50648352	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr15:50645920-50648439	GM18951	blood:	n/a	n/a
34	POLR2A	chr15:50645464-50650252	K562	blood:	n/a	n/a
35	POLR2A	chr15:50645912-50648548	HUVEC	blood vessel:	n/a	n/a
36	MYC	chr15:50645822-50648410	K562	blood:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
37	POLR2A	chr15:50645792-50648577	GM12878	blood:	n/a	n/a
38	POLR2A	chr15:50645959-50649428	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr15:50645995-50648531	MCF-7	breast:	n/a	n/a
40	POLR2A	chr15:50646787-50650247	K562	blood:	n/a	n/a
41	MYC	chr15:50645294-50648723	A549	lung:	n/a	chr15:50646903-50646913 chr15:50647687-50647697 chr15:50645298-50645305
42	RELA	chr15:50646896-50648514	GM18505	blood:	n/a	n/a
43	POLR2A	chr15:50646645-50648424	U87	brain:	n/a	n/a
44	POLR2A	chr15:50648238-50648500	GM12891	blood:	n/a	n/a
45	CHD1	chr15:50645756-50648859	H1-hESC	embryonic stem cell:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
46	REST	chr15:50646752-50648422	A549	lung:	n/a	n/a
47	POLR2A	chr15:50645493-50648538	GM19099	blood:	n/a	n/a
48	TBL1XR1	chr15:50646951-50648570	K562	blood:	n/a	n/a
49	CHD1	chr15:50645052-50649822	IMR90	lung:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
50	POLR2A	chr15:50645917-50648744	K562	blood:	n/a	n/a

No data

(count:40 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50645594..50649830-chr15:50754186..50757976,9	MCF-7	breast:
2	chr15:50646435..50649191-chr15:52859384..52862079,2	MCF-7	breast:
3	chr15:50473235..50476211-chr15:50645559..50648841,7	MCF-7	breast:
4	chr15:50643045..50650563-chr15:50756489..50761004,9	MCF-7	breast:
5	chr15:50647013..50649194-chr15:51198882..51202798,3	K562	blood:
6	chr15:50471646..50476620-chr15:50646050..50650091,9	MCF-7	breast:
7	chr15:50647163..50649970-chr15:50707470..50713022,5	MCF-7	breast:
8	chr15:50410321..50412713-chr15:50646391..50648447,2	MCF-7	breast:
9	chr15:50644389..50649393-chr15:50787180..50791359,7	MCF-7	breast:
10	chr15:50646264..50649073-chr17:62500886..62503658,2	MCF-7	breast:
11	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
12	chr15:50647220..50649637-chr15:50708002..50709799,2	K562	blood:
13	chr15:50513432..50516110-chr15:50646563..50649335,2	MCF-7	breast:
14	chr15:50646294..50648601-chr15:50837515..50839531,2	MCF-7	breast:
15	chr15:50552898..50556236-chr15:50646166..50649137,4	K562	blood:
16	chr11:66486776..66489307-chr15:50646648..50649417,2	MCF-7	breast:
17	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
18	chr12:108078496..108080358-chr15:50646042..50648645,2	MCF-7	breast:
19	chr15:50646198..50649019-chr15:50789771..50791870,3	MCF-7	breast:
20	chr15:49913123..49914709-chr15:50646540..50648629,2	K562	blood:
21	chr15:50645588..50649349-chr15:50728196..50732461,4	MCF-7	breast:
22	chr15:50646468..50650762-chr15:50786083..50789645,4	K562	blood:
23	chr15:50646359..50649336-chr15:50872616..50874692,3	MCF-7	breast:
24	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
25	chr15:50646133..50648665-chr7:100026247..100027987,2	MCF-7	breast:
26	chr15:50645261..50648746-chr15:51197475..51202828,11	MCF-7	breast:
27	chr15:50646763..50649574-chr8:128746981..128748587,2	MCF-7	breast:
28	chr15:50645260..50648664-chr15:50977679..50981268,7	MCF-7	breast:
29	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
30	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
31	chr15:50481284..50485703-chr15:50645023..50648855,4	MCF-7	breast:
32	chr15:50646196..50649637-chr15:50705519..50710625,4	K562	blood:
33	chr15:50647576..50648414-chr15:50716378..50717277,2	MCF-7	breast:
34	chr15:50645568..50648513-chr15:51198882..51201905,4	K562	blood:
35	chr15:50543402..50546278-chr15:50645480..50648581,3	MCF-7	breast:
36	chr15:50647970..50649936-chr15:50757455..50759138,2	K562	blood:
37	chr15:50648117..50650493-chr15:50779482..50782033,2	K562	blood:
38	chr15:50647443..50649396-chr15:50783549..50786868,3	MCF-7	breast:
39	chr11:20407767..20409374-chr15:50647141..50649461,2	MCF-7	breast:
40	chr15:50617729..50624931-chr15:50645125..50648613,9	MCF-7	breast:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50648297-50650501	ENSG00000244879
2	lnc-USP8-2	chr15:50648297-50648633	ENSG00000244879
3	lnc-USP8-2	chr15:50648297-50648567	ENSG00000244879.2
4	lnc-USP8-2	chr15:50648297-50648611	ENSG00000244879.2
5	lnc-USP8-2	chr15:50646371-50650503	NONHSAT042406
6	lnc-USP8-2	chr15:50648297-50650501	NONHSAT042411
7	lnc-USP8-2	chr15:50648295-50648637	NONHSAT042412
8	lnc-USP8-2	chr15:50648297-50650527	ENSG00000244879.2

No data

Variant related genes	Relation type
MIR4712	TF binding region
GABPB1	TF binding region
GABPB1-AS1	TF binding region
ENSG00000146834	Chromatin interaction
ENSG00000104047	Chromatin interaction
ENSG00000259618	Chromatin interaction
ENSG00000140287	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000185238	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000136045	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000243027	Chromatin interaction
ENSG00000200605	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000259465	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000259298	Chromatin interaction
ENSG00000242737	Chromatin interaction
ENSG00000252376	Chromatin interaction
ENSG00000170236	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000166262	Chromatin interaction
ENSG00000173898	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 26 )

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

rs_ID	r²[population]
rs1056681	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070770	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857071	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440601	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903381	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909202	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917303	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509458	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598020	1.00[ASN][1000 genomes]
rs2013885	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013888	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2033114	1.00[ASN][1000 genomes]
rs2414049	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450641	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45508400	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526045	0.81[AFR][1000 genomes]
rs62022563	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022564	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022565	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022567	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022569	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022570	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493426	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677143	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71424053	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72738935	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72738949	0.81[EUR][1000 genomes]
rs8034849	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920021	1.00[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs504781	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs504781	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs504781	CTD-3110H11.1	cis	Heart Left Ventricle	GTEx
rs504781	CTD-3110H11.1	cis	Artery Aorta	GTEx
rs504781	GABPB2	Cis_1M	lymphoblastoid	RTeQTL
rs504781	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs504781	GABPB1-AS1	cis	Artery Aorta	GTEx
rs504781	CTD-3110H11.1	cis	lung	GTEx
rs504781	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs504781	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs504781	GABPB1-AS1	cis	Whole Blood	GTEx
rs504781	CTD-3110H11.1	cis	Stomach	GTEx
rs504781	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs504781	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs504781	GABPB1-AS1	cis	Artery Tibial	GTEx
rs504781	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs504781	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs504781	GABPB1-AS1	cis	Thyroid	GTEx
rs504781	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs504781	GABPB1-AS1	cis	Stomach	GTEx
rs504781	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs504781	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs504781	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs504781	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs504781	CTD-3110H11.1	cis	Thyroid	GTEx
rs504781	GABPB1-AS1	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50644000-50648600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr15:50644000-50648600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr15:50644200-50648400	Active TSS	HSMMtube	muscle
4	chr15:50644200-50648600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:50644200-50648800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:50644400-50648400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:50644400-50648800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:50644400-50649000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:50644400-50649200	Active TSS	Fetal Brain Female	brain
10	chr15:50644400-50649400	Active TSS	NHLF	lung
11	chr15:50644600-50648800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:50644600-50649200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr15:50644600-50649200	Active TSS	GM12878-XiMat	blood
14	chr15:50644600-50649800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:50644800-50648400	Active TSS	Ovary	ovary
16	chr15:50644800-50648600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr15:50644800-50648600	Active TSS	HMEC	breast
18	chr15:50644800-50648800	Active TSS	Thymus	Thymus
19	chr15:50644800-50649200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:50644800-50649200	Active TSS	Right Ventricle	heart
21	chr15:50645000-50648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:50645000-50648400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr15:50645000-50648400	Active TSS	Aorta	Aorta
24	chr15:50645000-50648400	Active TSS	HSMM	muscle
25	chr15:50645000-50648400	Active TSS	K562	blood
26	chr15:50645000-50648600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:50645000-50648600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:50645000-50648600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr15:50645000-50648600	Active TSS	Fetal Intestine Large	intestine
30	chr15:50645000-50648600	Active TSS	Fetal Muscle Trunk	muscle
31	chr15:50645000-50648600	Active TSS	Stomach Smooth Muscle	stomach
32	chr15:50645000-50648800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:50645000-50649000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:50645000-50649000	Active TSS	Primary T cells fromperipheralblood	blood
35	chr15:50645000-50649000	Active TSS	Fetal Muscle Leg	muscle
36	chr15:50645000-50649000	Active TSS	NHDF-Ad	bronchial
37	chr15:50645000-50649200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:50645000-50649200	Active TSS	Fetal Thymus	thymus
39	chr15:50645000-50649600	Active TSS	Psoas Muscle	Psoas
40	chr15:50645200-50648400	Active TSS	Osteobl	bone
41	chr15:50645200-50648600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr15:50645200-50648600	Active TSS	Fetal Stomach	stomach
43	chr15:50645200-50648600	Active TSS	NH-A	brain
44	chr15:50645200-50648600	Active TSS	NHEK	skin
45	chr15:50645200-50649000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:50645400-50648400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:50645400-50648600	Active TSS	Fetal Intestine Small	intestine
48	chr15:50645400-50648800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:50645400-50649400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr15:50645600-50648400	Active TSS	Skeletal Muscle Male	skeletal muscle

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