Variant report

Variant	rs9920783
Chromosome Location	chr15:78219278-78219279
allele	C/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	POLR2A	chr15:78219018-78219311	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr15:78219249-78219491	MCF-7	breast:	n/a	chr15:78219292-78219306 chr15:78219293-78219307
3	TBP	chr15:78219097-78219320	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:78218968-78219372	H1-hESC	embryonic stem cell:	n/a	n/a
5	PAX5	chr15:78219065-78219338	GM12878	blood:	n/a	chr15:78219302-78219321
6	PAX5	chr15:78219022-78219452	GM12878	blood:	n/a	chr15:78219302-78219321
7	POU2F2	chr15:78219014-78219448	GM12878	blood:	n/a	n/a
8	SP1	chr15:78219132-78219453	GM12878	blood:	n/a	chr15:78219402-78219412 chr15:78219402-78219412 chr15:78219252-78219262 chr15:78219398-78219412 chr15:78219402-78219411 chr15:78219403-78219412 chr15:78219401-78219413 chr15:78219142-78219156 chr15:78219309-78219319 chr15:78219267-78219288 chr15:78219401-78219413 chr15:78219384-78219393 chr15:78219403-78219412 chr15:78219252-78219262 chr15:78219382-78219394
9	MAZ	chr15:78219248-78219450	K562	blood:	n/a	n/a
10	SP1	chr15:78219030-78219423	GM12878	blood:	n/a	chr15:78219402-78219412 chr15:78219402-78219412 chr15:78219252-78219262 chr15:78219398-78219412 chr15:78219402-78219411 chr15:78219403-78219412 chr15:78219401-78219413 chr15:78219142-78219156 chr15:78219309-78219319 chr15:78219267-78219288 chr15:78219401-78219413 chr15:78219384-78219393 chr15:78219403-78219412 chr15:78219252-78219262 chr15:78219382-78219394
11	ATF1	chr15:78219190-78219467	K562	blood:	n/a	n/a
12	TBP	chr15:78219256-78219287	K562	blood:	n/a	n/a
13	TAF1	chr15:78218955-78219424	H1-hESC	embryonic stem cell:	n/a	n/a
14	IRF1	chr15:78219207-78219482	K562	blood:	n/a	chr15:78219380-78219394 chr15:78219401-78219415 chr15:78219295-78219309 chr15:78219308-78219322
15	TAF1	chr15:78219037-78219378	Hela-S3	cervix:	n/a	n/a
16	MAX	chr15:78219167-78219470	K562	blood:	n/a	n/a
17	POLR2A	chr15:78218940-78219343	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF7L2	chr15:78219117-78219486	HCT-116	colon:	n/a	chr15:78219292-78219306 chr15:78219293-78219307
19	RCOR1	chr15:78219150-78219464	K562	blood:	n/a	n/a
20	MYC	chr15:78219264-78219478	K562	blood:	n/a	n/a
21	POLR2A	chr15:78218092-78219493	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF7L2	chr15:78219130-78219482	Hela-S3	cervix:	n/a	chr15:78219292-78219306 chr15:78219293-78219307
23	JUND	chr15:78219241-78219488	K562	blood:	n/a	chr15:78219347-78219356 chr15:78219276-78219285
24	POLR2A	chr15:78219126-78219339	K562	blood:	n/a	n/a
25	POLR2A	chr15:78219076-78219348	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr15:78219105-78219392	K562	blood:	n/a	n/a
27	JUN	chr15:78219246-78219519	K562	blood:	n/a	chr15:78219347-78219356 chr15:78219276-78219285
28	POLR2A	chr15:78219058-78219344	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr15:78218868-78219348	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:78219273-78219323	NHBE	bronchial:	n/a
2	chr15:78219273-78219323	K562	blood:	n/a
3	chr15:78219273-78219323	AG10803	skin:	n/a
4	chr15:78219273-78219323	AG09319	gingival:	n/a
5	chr15:78219273-78219323	HIPEpiC	eye:	n/a
6	chr15:78219273-78219323	SK-N-MC	brain:	n/a
7	chr15:78219273-78219323	SK-N-SH	brain:	n/a
8	chr15:78219273-78219323	LNCaP	prostate:	n/a
9	chr15:78219273-78219323	NB4	blood:	n/a
10	chr15:78219273-78219323	HCPEpiC	choroid plexus:	n/a
11	chr15:78219273-78219323	GM19239	blood:	n/a
12	chr15:78219273-78219323	GM12878	blood:	n/a
13	chr15:78219273-78219323	HAEpiC	amniotic membrane:	n/a
14	chr15:78219273-78219323	T-47D	breast:	n/a
15	chr15:78219273-78219323	HNPCEpiC	eye:	n/a
16	chr15:78219273-78219323	CMK	blood:	n/a
17	chr15:78219273-78219323	GM12891	blood:	n/a
18	chr15:78219273-78219323	HRCEpiC	kidney:	n/a
19	chr15:78219273-78219323	Jurkat	blood:	n/a
20	chr15:78219273-78219323	ovcar-3	ovarian:	n/a
21	chr15:78219273-78219323	MCF-7	breast:	n/a
22	chr15:78219273-78219323	H1-hESC	embryonic stem cell:	embryo
23	chr15:78219273-78219323	AG04450	lung:	fetal
24	chr15:78219273-78219323	MCF10A-Er-Src	breast:	n/a
25	chr15:78219273-78219323	NH-A	brain:	n/a
26	chr15:78219273-78219323	HL-60	blood:	n/a
27	chr15:78219273-78219323	HEK293	kidney:	embryo
28	chr15:78219273-78219323	Hepatocyte	liver:	n/a
29	chr15:78219273-78219323	NHDF-neo	bronchial:	n/a
30	chr15:78219273-78219323	HRPEpiC	eye:	n/a
31	chr15:78219273-78219323	HMEC	breast:	n/a
32	chr15:78219273-78219323	GM12892	blood:	n/a
33	chr15:78219273-78219323	PFSK-1	brain:	n/a
34	chr15:78219273-78219323	HCT-116	colon:	n/a
35	chr15:78219273-78219323	Caco-2	colon:	n/a
36	chr15:78219273-78219323	A549	lung:	n/a
37	chr15:78219273-78219323	HRE	kidney:	n/a
38	chr15:78219273-78219323	HCM	heart:	n/a
39	chr15:78219273-78219323	HPAEpiC	pulmonary alveolar:	n/a
40	chr15:78219273-78219323	AoSMC	blood vessel:	n/a
41	chr15:78219273-78219323	U87	brain:	n/a
42	chr15:78219273-78219323	PANC-1	pancreas:	n/a
43	chr15:78219273-78219323	ECC-1	luminal epithelium:	n/a
44	chr15:78219273-78219323	SAEC	small airway:	n/a
45	chr15:78219273-78219323	HUVEC	blood vessel:	n/a
46	chr15:78219273-78219323	HepG2	liver:	n/a
47	chr15:78219273-78219323	RPTEC	kidney:	n/a
48	chr15:78219273-78219323	HCF	heart:	n/a
49	chr15:78219273-78219323	AG09309	skin:	n/a
50	chr15:78219273-78219323	HEEpiC	esophagus:	n/a

Variant related genes	Relation type
ENSG00000260776	TF binding region
ENSG00000260776	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs28520639	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28540428	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28754523	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4261494	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4480764	0.89[ASN][1000 genomes]
rs57239225	0.86[ASN][1000 genomes]
rs72732513	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72732516	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9920532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv833062	chr15:78035206-78220358	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv904426	chr15:78090630-78264164	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904427	chr15:78129964-78251431	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv976954	chr15:78153346-78255825	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1046383	chr15:78153850-78229596	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv904428	chr15:78156238-78230906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv904429	chr15:78160362-78251431	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv1823600	chr15:78200594-78219757	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv18540	chr15:78202973-78227329	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv9281	chr15:78213140-78225495	Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9920783	RP11-114H24.2	cis	Esophagus Muscularis	GTEx
rs9920783	RP11-114H24.4	cis	Thyroid	GTEx
rs9920783	RP11-114H24.2	cis	Nerve Tibial	GTEx
rs9920783	RP11-114H24.2	cis	Thyroid	GTEx
rs9920783	RP11-114H24.2	cis	Muscle Skeletal	GTEx
rs9920783	RP11-114H24.2	cis	lung	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78203200-78220200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:78203200-78227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:78219000-78222800	Weak transcription	HepG2	liver
4	chr15:78219200-78222600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:78219200-78228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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