Variant report

Variant	rs16940768
Chromosome Location	chr15:59063506-59063507
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	SIN3AK20	chr15:59063025-59063591	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr15:59062367-59063941	K562	blood:	n/a	n/a
3	CTCF	chr15:59063358-59063601	MCF-7	breast:	n/a	n/a
4	SIN3A	chr15:59062738-59064694	H1-hESC	embryonic stem cell:	n/a	chr15:59063345-59063354 chr15:59063347-59063356
5	CTCF	chr15:59063380-59063530	HL-60	blood:	n/a	n/a
6	NFYB	chr15:59063093-59063541	K562	blood:	n/a	n/a
7	JUND	chr15:59063001-59063560	HepG2	liver:	n/a	n/a
8	TEAD4	chr15:59063052-59063685	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr15:59063071-59063873	HCT-116	colon:	n/a	n/a
10	RFX5	chr15:59062909-59063618	GM12878	blood:	n/a	n/a
11	ZNF263	chr15:59062933-59064648	HEK293-T-REx	kidney:	n/a	chr15:59064250-59064271
12	E2F6	chr15:59063215-59063521	K562	blood:	n/a	chr15:59063434-59063448
13	TBL1XR1	chr15:59062778-59063786	K562	blood:	n/a	n/a
14	PAX5	chr15:59063030-59063585	GM12878	blood:	n/a	chr15:59063441-59063450 chr15:59063437-59063446 chr15:59063439-59063448
15	RCOR1	chr15:59062569-59064546	K562	blood:	n/a	n/a
16	CTCF	chr15:59063420-59063570	GM12875	blood:	n/a	n/a
17	YY1	chr15:59063032-59064439	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr15:59062796-59063985	HUVEC	blood vessel:	n/a	n/a
19	ZBTB33	chr15:59062911-59063688	A549	lung:	n/a	n/a
20	USF1	chr15:59063065-59063608	A549	lung:	n/a	n/a
21	KAP1	chr15:59062827-59063560	U2OS	brain:	n/a	n/a
22	E2F4	chr15:59063020-59064437	K562	blood:	n/a	chr15:59063434-59063448 chr15:59063577-59063586
23	TAF1	chr15:59062974-59063750	MCF-7	breast:	n/a	n/a
24	CTCF	chr15:59063440-59063590	HCT-116	colon:	n/a	n/a
25	POLR2A	chr15:59062764-59064607	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr15:59063301-59063652	SK-N-SH	brain:	n/a	n/a
27	EBF1	chr15:59062721-59063609	GM12878	blood:	n/a	n/a
28	SP1	chr15:59062681-59063814	A549	lung:	n/a	chr15:59063577-59063586 chr15:59063284-59063294 chr15:59063284-59063294
29	MYC	chr15:59063074-59063557	HUVEC	blood vessel:	n/a	chr15:59063346-59063355 chr15:59063346-59063356 chr15:59063345-59063356 chr15:59063346-59063355 chr15:59063345-59063355 chr15:59063346-59063355 chr15:59063345-59063356 chr15:59063348-59063357
30	POLR2A	chr15:59062992-59063760	A549	lung:	n/a	n/a
31	POLR2A	chr15:59062689-59063991	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr15:59063420-59063570	Caco-2	colon:	n/a	n/a
33	ELF1	chr15:59062965-59063807	GM12878	blood:	n/a	n/a
34	TBP	chr15:59062687-59063738	HepG2	liver:	n/a	n/a
35	POLR2A	chr15:59062936-59063762	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr15:59062773-59063830	HL-60	blood:	n/a	n/a
37	TBP	chr15:59062591-59063687	Hela-S3	cervix:	n/a	n/a
38	CREB1	chr15:59062746-59064000	HepG2	liver:	n/a	n/a
39	USF1	chr15:59063026-59063602	A549	lung:	n/a	n/a
40	UBTF	chr15:59062570-59064626	K562	blood:	n/a	n/a
41	ELF1	chr15:59062903-59063746	MCF-7	breast:	n/a	n/a
42	SMARCB1	chr15:59062941-59064472	Hela-S3	cervix:	n/a	n/a
43	PBX3	chr15:59062919-59063832	A549	lung:	n/a	n/a
44	TAF7	chr15:59063028-59063738	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr15:59063282-59064021	K562	blood:	n/a	n/a
46	CTCF	chr15:59063290-59063907	GM12878	blood:	n/a	n/a
47	JUND	chr15:59062616-59064449	H1-hESC	embryonic stem cell:	n/a	chr15:59063580-59063589
48	MAX	chr15:59063013-59063638	MCF-7	breast:	n/a	chr15:59063346-59063355 chr15:59063346-59063356 chr15:59063345-59063356 chr15:59063346-59063355 chr15:59063345-59063355 chr15:59063346-59063355 chr15:59063345-59063356 chr15:59063348-59063357
49	TFAP2C	chr15:59062696-59064580	Hela-S3	cervix:	n/a	chr15:59064224-59064239
50	USF2	chr15:59062930-59063564	GM12878	blood:	n/a	chr15:59063344-59063355

No.	Distal block	Cell Line	Cell type
1	chr15:59061870..59064465-chr15:59224425..59227494,5	K562	blood:
2	chr15:59062926..59063673-chr6:32811899..32812879,2	Hela-S3	cervix:
3	chr15:59061712..59064488-chr15:59178344..59181230,2	K562	blood:
4	chr15:59062962..59064061-chr17:73775541..73776117,3	Hela-S3	cervix:
5	chr10:60145015..60145625-chr15:59063219..59063805,2	Hela-S3	cervix:
6	chr15:58622254..58626014-chr15:59062445..59064794,4	K562	blood:
7	chr15:59051351..59055079-chr15:59061641..59063693,4	K562	blood:
8	chr14:75642948..75643449-chr15:59063013..59063683,2	Hela-S3	cervix:
9	chr15:59052627..59055079-chr15:59061662..59063562,2	K562	blood:
10	chr15:59063370..59063986-chr5:34929328..34930251,2	Hela-S3	cervix:
11	chr15:58549388..58551479-chr15:59062229..59064301,2	K562	blood:
12	chr15:59040077..59045685-chr15:59061303..59067063,14	K562	blood:
13	chr15:59061037..59064884-chr15:59224205..59227723,8	K562	blood:
14	chr15:59040618..59043171-chr15:59061931..59064461,2	MCF-7	breast:
15	chr15:59038832..59043387-chr15:59060936..59065101,7	K562	blood:

Variant related genes	Relation type
FAM63B	TF binding region
ENSG00000245975	TF binding region
ENSG00000204261	Chromatin interaction
ENSG00000170348	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000168724	Chromatin interaction
ENSG00000108064	Chromatin interaction
ENSG00000128918	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000137845	Chromatin interaction
ENSG00000240065	Chromatin interaction
ENSG00000200318	Chromatin interaction
ENSG00000204264	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs16940570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940638	1.00[EUR][1000 genomes]
rs16940723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940751	0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16940766	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940771	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953381	1.00[AMR][1000 genomes]
rs2414609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55939313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56039925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56357958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56935364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56942476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57083702	1.00[EUR][1000 genomes]
rs57845422	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58667875	1.00[AMR][1000 genomes]
rs58937576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61678411	1.00[EUR][1000 genomes]
rs6494024	1.00[EUR][1000 genomes]
rs7163948	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7164104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168066	0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7172673	1.00[EUR][1000 genomes]
rs7173048	1.00[EUR][1000 genomes]
rs7174279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7175610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183811	1.00[AMR][1000 genomes]
rs74016920	1.00[EUR][1000 genomes]
rs74016943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74016946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74016947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017259	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017270	1.00[EUR][1000 genomes]
rs74017281	1.00[EUR][1000 genomes]
rs74017286	1.00[EUR][1000 genomes]
rs74017293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017301	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74018920	1.00[EUR][1000 genomes]
rs74021007	1.00[AMR][1000 genomes]
rs74021013	1.00[AMR][1000 genomes]
rs8025475	1.00[EUR][1000 genomes]
rs8027618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8028872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8029869	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8032451	1.00[EUR][1000 genomes]
rs8033613	1.00[EUR][1000 genomes]
rs8043275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs881117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16940768	ENSG00000128923	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59062200-59063600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:59062200-59063600	Active TSS	HepG2	liver
3	chr15:59062200-59064400	Active TSS	Hela-S3	cervix
4	chr15:59062200-59064800	Active TSS	HMEC	breast
5	chr15:59062200-59065000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:59062200-59065000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:59062200-59065000	Active TSS	K562	blood
8	chr15:59062200-59065400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:59062200-59066000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:59062200-59066000	Active TSS	NHLF	lung
11	chr15:59062200-59066200	Active TSS	HSMMtube	muscle
12	chr15:59062200-59067800	Active TSS	GM12878-XiMat	blood
13	chr15:59062400-59064200	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr15:59062400-59064800	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr15:59062400-59064800	Active TSS	Brain Substantia Nigra	brain
16	chr15:59062400-59065200	Active TSS	Brain Hippocampus Middle	brain
17	chr15:59062400-59065400	Active TSS	Brain Germinal Matrix	brain
18	chr15:59062400-59065800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr15:59062400-59065800	Active TSS	Psoas Muscle	Psoas
20	chr15:59062400-59066000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:59062400-59066200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:59062400-59066400	Active TSS	Right Ventricle	heart
23	chr15:59062400-59066600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr15:59062400-59067400	Active TSS	Right Atrium	heart
25	chr15:59062400-59067800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:59062600-59064200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr15:59062600-59064400	Active TSS	Pancreas	Pancrea
28	chr15:59062600-59064600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:59062600-59064600	Active TSS	Esophagus	oesophagus
30	chr15:59062600-59064600	Active TSS	Lung	lung
31	chr15:59062600-59064800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr15:59062600-59064800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:59062600-59064800	Active TSS	Fetal Muscle Trunk	muscle
34	chr15:59062600-59065000	Active TSS	Brain Anterior Caudate	brain
35	chr15:59062600-59065000	Active TSS	Stomach Mucosa	stomach
36	chr15:59062600-59065400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:59062600-59065600	Active TSS	Colonic Mucosa	Colon
38	chr15:59062600-59065800	Active TSS	H1 Cell Line	embryonic stem cell
39	chr15:59062600-59065800	Active TSS	Aorta	Aorta
40	chr15:59062600-59065800	Active TSS	Left Ventricle	heart
41	chr15:59062600-59066000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:59062600-59066400	Active TSS	Ovary	ovary
43	chr15:59062800-59063600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:59062800-59063800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:59062800-59064400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:59062800-59064400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:59062800-59064400	Active TSS	Small Intestine	intestine
48	chr15:59062800-59064600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:59062800-59064600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:59062800-59064600	Active TSS	Gastric	stomach

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