Variant report

Variant	rs2414609
Chromosome Location	chr15:59042452-59042453
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	MAX	chr15:59041685-59042656	GM12878	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
2	USF1	chr15:59041687-59042563	A549	lung:	n/a	chr15:59042041-59042052 chr15:59042462-59042478
3	GABPA	chr15:59041716-59042460	MCF-7	breast:	n/a	chr15:59042129-59042140 chr15:59042136-59042145 chr15:59042126-59042140 chr15:59042129-59042138 chr15:59042129-59042143 chr15:59042131-59042140
4	TCF12	chr15:59041603-59042618	ECC-1	luminal epithelium:	n/a	chr15:59042464-59042474
5	CREB1	chr15:59041564-59042616	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:59041579-59042534	K562	blood:	n/a	n/a
7	MXI1	chr15:59040155-59043064	IMR90	lung:	n/a	chr15:59042043-59042052
8	TBL1XR1	chr15:59041339-59042532	K562	blood:	n/a	n/a
9	TBL1XR1	chr15:59041464-59042534	K562	blood:	n/a	n/a
10	CREB1	chr15:59041899-59042581	A549	lung:	n/a	n/a
11	POLR2A	chr15:59041628-59042557	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr15:59041550-59042537	K562	blood:	n/a	n/a
13	JUND	chr15:59040796-59042538	K562	blood:	n/a	chr15:59041444-59041453 chr15:59042213-59042222 chr15:59041417-59041426
14	POLR2A	chr15:59041704-59042586	GM12878	blood:	n/a	n/a
15	MAZ	chr15:59040536-59042601	GM12878	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
16	PML	chr15:59041633-59042570	K562	blood:	n/a	n/a
17	ELF1	chr15:59041685-59042475	MCF-7	breast:	n/a	n/a
18	EP300	chr15:59041847-59042492	GM12878	blood:	n/a	chr15:59042185-59042201 chr15:59042384-59042398 chr15:59042381-59042395
19	BHLHE40	chr15:59040938-59042760	K562	blood:	n/a	chr15:59041307-59041323 chr15:59042462-59042478
20	TAF1	chr15:59041614-59042565	A549	lung:	n/a	n/a
21	POLR2A	chr15:59042176-59042455	GM12891	blood:	n/a	n/a
22	GABPA	chr15:59041664-59042496	A549	lung:	n/a	chr15:59042129-59042140 chr15:59042136-59042145 chr15:59042126-59042140 chr15:59042129-59042138 chr15:59042129-59042143 chr15:59042131-59042140
23	TAF1	chr15:59041659-59042489	PFSK-1	brain:	n/a	n/a
24	TAL1	chr15:59041873-59042515	K562	blood:	n/a	n/a
25	WRNIP1	chr15:59042209-59042504	GM12878	blood:	n/a	n/a
26	YY1	chr15:59041693-59042543	SK-N-SH_RA	brain:	n/a	n/a
27	YY1	chr15:59041799-59042617	SK-N-SH	brain:	n/a	n/a
28	MAX	chr15:59041140-59042508	HepG2	liver:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
29	POLR2A	chr15:59040980-59043115	HepG2	liver:	n/a	n/a
30	MAX	chr15:59040970-59042559	A549	lung:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
31	MAZ	chr15:59040253-59043183	IMR90	lung:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
32	ELF1	chr15:59041589-59042475	GM12878	blood:	n/a	n/a
33	ELF1	chr15:59041661-59042547	HCT-116	colon:	n/a	n/a
34	POLR2A	chr15:59041518-59042555	MCF-7	breast:	n/a	n/a
35	MAX	chr15:59040686-59042861	K562	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
36	MYC	chr15:59040706-59042728	NB4	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
37	HA-E2F1	chr15:59040974-59042493	MCF-7	breast:	n/a	chr15:59042167-59042177 chr15:59042242-59042254 chr15:59042214-59042223 chr15:59041445-59041454 chr15:59042130-59042139 chr15:59041445-59041457 chr15:59041416-59041425
38	USF1	chr15:59041712-59042713	A549	lung:	n/a	chr15:59042041-59042052 chr15:59042462-59042478
39	POLR2A	chr15:59041624-59042709	U87	brain:	n/a	n/a
40	MAX	chr15:59041670-59042672	SK-N-SH	brain:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
41	POLR2A	chr15:59042133-59042507	Hela-S3	cervix:	n/a	n/a
42	CREB1	chr15:59041484-59042497	A549	lung:	n/a	n/a
43	MAZ	chr15:59040692-59042696	K562	blood:	n/a	chr15:59042042-59042051 chr15:59042041-59042052 chr15:59042042-59042051 chr15:59042042-59042051
44	CREB1	chr15:59041858-59042509	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr15:59041622-59042702	HCT-116	colon:	n/a	n/a
46	PML	chr15:59041627-59042705	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:59040755-59042510	Raji	blood:	n/a	n/a
48	SRF	chr15:59041641-59042512	ECC-1	luminal epithelium:	n/a	n/a
49	STAT3	chr15:59042341-59042726	GM12878	blood:	n/a	n/a
50	POLR2A	chr15:59040660-59042553	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:59040077..59045685-chr15:59061303..59067063,14	K562	blood:
2	chr15:59040771..59044388-chr15:59046627..59050183,4	K562	blood:
3	chr15:59042046..59047020-chr15:59050998..59056418,7	K562	blood:
4	chr15:59040867..59044243-chr15:59224539..59228117,4	K562	blood:
5	chr15:59038832..59043387-chr15:59060936..59065101,7	K562	blood:
6	chr15:59042171..59043978-chr15:59046627..59049380,3	K562	blood:
7	chr15:59040618..59043171-chr15:59061931..59064461,2	MCF-7	breast:
8	chr15:59040332..59042868-chr15:59224764..59227201,2	MCF-7	breast:

Variant related genes	Relation type
ADAM10	TF binding region
ENSG00000128923	Chromatin interaction
ENSG00000245975	Chromatin interaction
ENSG00000200318	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000259173	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

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	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940751	1.00[EUR][1000 genomes]
rs16940766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940771	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953381	1.00[AMR][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	1.00[EUR][1000 genomes]
rs58667875	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58937576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61678411	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6494024	1.00[EUR][1000 genomes]
rs7163948	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	0.84[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	0.84[AFR][1000 genomes];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	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74017293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017296	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017297	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017298	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017300	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017301	1.00[EUR][1000 genomes]
rs74017302	0.88[AFR][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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8029869	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	0.83[AFR][1000 genomes];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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59037800-59042600	Active TSS	HSMMtube	muscle
2	chr15:59037800-59043000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:59038000-59042800	Active TSS	Right Atrium	heart
4	chr15:59038000-59043000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:59038200-59042600	Active TSS	NHLF	lung
6	chr15:59038400-59042800	Active TSS	HSMM	muscle
7	chr15:59038400-59043200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:59038600-59042800	Active TSS	Right Ventricle	heart
9	chr15:59038800-59042600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:59038800-59042600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:59038800-59043200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr15:59039000-59042800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:59039000-59042800	Active TSS	K562	blood
14	chr15:59039000-59043000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:59039000-59043200	Active TSS	NHDF-Ad	bronchial
16	chr15:59039200-59042800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:59039400-59042600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:59039400-59042800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:59039400-59042800	Active TSS	Aorta	Aorta
20	chr15:59039400-59042800	Active TSS	Fetal Kidney	kidney
21	chr15:59039400-59043000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr15:59039600-59042600	Active TSS	Brain Substantia Nigra	brain
23	chr15:59039600-59043200	Active TSS	Brain Germinal Matrix	brain
24	chr15:59039800-59042600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:59039800-59042600	Active TSS	Brain Angular Gyrus	brain
26	chr15:59039800-59042600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr15:59039800-59042600	Active TSS	Fetal Brain Female	brain
28	chr15:59039800-59042800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:59039800-59042800	Active TSS	Brain Hippocampus Middle	brain
30	chr15:59039800-59042800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr15:59039800-59043000	Active TSS	Brain Cingulate Gyrus	brain
32	chr15:59039800-59043000	Active TSS	Fetal Intestine Large	intestine
33	chr15:59039800-59043200	Active TSS	Stomach Smooth Muscle	stomach
34	chr15:59040000-59042600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr15:59040000-59042600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr15:59040000-59042600	Active TSS	NH-A	brain
37	chr15:59040000-59042800	Active TSS	Colonic Mucosa	Colon
38	chr15:59040000-59042800	Active TSS	Fetal Lung	lung
39	chr15:59040000-59043200	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr15:59040000-59043200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:59040200-59042600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:59040200-59042600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:59040200-59042600	Active TSS	Colon Smooth Muscle	Colon
44	chr15:59040200-59042600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr15:59040200-59042600	Active TSS	Fetal Heart	heart
46	chr15:59040200-59042600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr15:59040200-59042600	Active TSS	Rectal Smooth Muscle	rectum
48	chr15:59040200-59042600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr15:59040200-59042800	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr15:59040200-59042800	Active TSS	Fetal Muscle Trunk	muscle

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