Variant report

Variant	rs28559610
Chromosome Location	chr15:59064014-59064015
allele	A/G
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	SIN3A	chr15:59062738-59064694	H1-hESC	embryonic stem cell:	n/a	chr15:59063345-59063354 chr15:59063347-59063356
2	ZNF263	chr15:59062933-59064648	HEK293-T-REx	kidney:	n/a	chr15:59064250-59064271
3	RCOR1	chr15:59062569-59064546	K562	blood:	n/a	n/a
4	YY1	chr15:59063032-59064439	SK-N-SH	brain:	n/a	n/a
5	E2F6	chr15:59063864-59064062	K562	blood:	n/a	n/a
6	E2F4	chr15:59063020-59064437	K562	blood:	n/a	chr15:59063434-59063448 chr15:59063577-59063586
7	CTCF	chr15:59063940-59064090	GM12865	blood:	n/a	n/a
8	POLR2A	chr15:59062764-59064607	H1-neurons	neurons:	n/a	n/a
9	MXI1	chr15:59063977-59064212	H1-hESC	embryonic stem cell:	n/a	n/a
10	UBTF	chr15:59062570-59064626	K562	blood:	n/a	n/a
11	SMARCB1	chr15:59062941-59064472	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr15:59063282-59064021	K562	blood:	n/a	n/a
13	JUND	chr15:59062616-59064449	H1-hESC	embryonic stem cell:	n/a	chr15:59063580-59063589
14	TFAP2C	chr15:59062696-59064580	Hela-S3	cervix:	n/a	chr15:59064224-59064239
15	MAX	chr15:59062652-59064516	Hela-S3	cervix:	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
16	MAX	chr15:59062656-59064499	K562	blood:	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
17	CTCF	chr15:59063980-59064130	GM12878	blood:	n/a	n/a
18	HA-E2F1	chr15:59063096-59064090	Hela-S3	cervix:	n/a	chr15:59063434-59063448 chr15:59063577-59063586
19	ZBTB7A	chr15:59062989-59064439	ECC-1	luminal epithelium:	n/a	n/a
20	YY1	chr15:59062798-59064106	HepG2	liver:	n/a	n/a
21	MAX	chr15:59062630-59064571	A549	lung:	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
22	CTCF	chr15:59064000-59064150	GM12867	blood:	n/a	n/a
23	POLR2A	chr15:59062602-59064692	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr15:59062734-59064333	H1-hESC	embryonic stem cell:	n/a	chr15:59063574-59063584
25	RCOR1	chr15:59062723-59064634	Hela-S3	cervix:	n/a	n/a
26	MAZ	chr15:59062789-59064575	K562	blood:	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
27	TAF1	chr15:59062997-59064049	HepG2	liver:	n/a	n/a
28	CREB1	chr15:59062970-59064336	A549	lung:	n/a	n/a
29	YY1	chr15:59063042-59064347	GM12892	blood:	n/a	n/a
30	MAZ	chr15:59062790-59064564	Hela-S3	cervix:	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
31	CHD1	chr15:59063451-59064323	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF1	chr15:59062900-59064244	ECC-1	luminal epithelium:	n/a	n/a
33	NFIC	chr15:59062651-59064339	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr15:59063999-59064383	MCF-7	breast:	n/a	n/a
35	SP1	chr15:59062553-59064069	A549	lung:	n/a	chr15:59063577-59063586 chr15:59063284-59063294 chr15:59063284-59063294
36	ZNF143	chr15:59063961-59064449	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAZ	chr15:59062433-59064689	IMR90	lung:	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
38	E2F1	chr15:59063111-59064359	Hela-S3	cervix:	n/a	chr15:59063434-59063448 chr15:59063577-59063586
39	CCNT2	chr15:59062498-59064377	K562	blood:	n/a	n/a
40	RAD21	chr15:59062678-59064479	IMR90	lung:	n/a	chr15:59063574-59063584
41	POLR2A	chr15:59062620-59064515	Hela-S3	cervix:	n/a	n/a
42	ZNF143	chr15:59062716-59064036	Hela-S3	cervix:	n/a	n/a
43	EBF1	chr15:59063861-59064096	GM12878	blood:	n/a	n/a
44	YY1	chr15:59062957-59064347	H1-hESC	embryonic stem cell:	n/a	n/a
45	TEAD4	chr15:59063894-59064220	H1-hESC	embryonic stem cell:	n/a	n/a
46	GATA3	chr15:59062728-59064605	A549	lung:	n/a	n/a
47	MXI1	chr15:59062451-59064723	IMR90	lung:	n/a	chr15:59063345-59063354 chr15:59063345-59063354 chr15:59063347-59063356
48	TBL1XR1	chr15:59063897-59064045	K562	blood:	n/a	n/a
49	POLR2A	chr15:59062730-59064289	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr15:59062939-59064288	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:59061870..59064465-chr15:59224425..59227494,5	K562	blood:
2	chr15:59061712..59064488-chr15:59178344..59181230,2	K562	blood:
3	chr15:59063778..59064335-chr6:36085361..36086329,2	NB4	blood:
4	chr1:146556597..146557184-chr15:59063588..59064562,2	Hela-S3	cervix:
5	chr15:59062962..59064061-chr17:73775541..73776117,3	Hela-S3	cervix:
6	chr15:58622254..58626014-chr15:59062445..59064794,4	K562	blood:
7	chr15:59063628..59066119-chr15:59070101..59071953,2	MCF-7	breast:
8	chr15:58549388..58551479-chr15:59062229..59064301,2	K562	blood:
9	chr15:59040077..59045685-chr15:59061303..59067063,14	K562	blood:
10	chr15:59061037..59064884-chr15:59224205..59227723,8	K562	blood:
11	chr15:59040618..59043171-chr15:59061931..59064461,2	MCF-7	breast:
12	chr15:59038832..59043387-chr15:59060936..59065101,7	K562	blood:

Variant related genes	Relation type
ENSG00000245975	TF binding region
ENSG00000128918	Chromatin interaction
ENSG00000137845	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000132475	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16940595	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16940604	1.00[AMR][1000 genomes]
rs16940675	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16940727	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16953391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57735680	1.00[AMR][1000 genomes]
rs57815388	1.00[AMR][1000 genomes]
rs61339643	1.00[AMR][1000 genomes]
rs73414812	1.00[AMR][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

No data

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

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

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