Variant report

Variant	rs1693516
Chromosome Location	chr15:52821633-52821634
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	NR2F2	chr15:52820508-52821958	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:52820697-52821708	GM19099	blood:	n/a	n/a
3	POLR2A	chr15:52820010-52822087	H1-neurons	neurons:	n/a	n/a
4	STAT5A	chr15:52821471-52821886	GM12878	blood:	n/a	chr15:52821680-52821703
5	POLR2A	chr15:52820697-52821641	HUVEC	blood vessel:	n/a	n/a
6	ELF1	chr15:52820335-52821802	GM12878	blood:	n/a	chr15:52820882-52820894 chr15:52821461-52821473 chr15:52821465-52821474 chr15:52821037-52821049
7	YY1	chr15:52820621-52821746	GM12892	blood:	n/a	chr15:52820959-52820968 chr15:52821454-52821468 chr15:52820735-52820746 chr15:52821085-52821096 chr15:52821460-52821474 chr15:52821465-52821474 chr15:52821457-52821471 chr15:52821462-52821471 chr15:52821462-52821473 chr15:52821086-52821100
8	TAF1	chr15:52821199-52821767	H1-neurons	neurons:	n/a	n/a
9	SMC3	chr15:52820946-52821729	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:52820690-52821948	U87	brain:	n/a	n/a
11	CHD2	chr15:52820914-52821649	Hela-S3	cervix:	n/a	chr15:52821471-52821481
12	EBF1	chr15:52821177-52821643	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:52820422-52821731	GM18951	blood:	n/a	n/a
14	ZNF263	chr15:52821318-52821818	HEK293-T-REx	kidney:	n/a	chr15:52821346-52821355
15	POLR2A	chr15:52821149-52821682	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:52820676-52821666	GM15510	blood:	n/a	n/a
17	POLR2A	chr15:52820744-52821645	MCF-7	breast:	n/a	n/a
18	TBP	chr15:52820362-52821995	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr15:52820788-52821659	GM18526	blood:	n/a	n/a
20	JUND	chr15:52821385-52821867	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr15:52820625-52821762	GM12878	blood:	n/a	chr15:52820959-52820968 chr15:52821454-52821468 chr15:52820735-52820746 chr15:52821085-52821096 chr15:52821460-52821474 chr15:52821465-52821474 chr15:52821457-52821471 chr15:52821462-52821471 chr15:52821462-52821473 chr15:52821086-52821100
22	STAT1	chr15:52821205-52821668	GM12878	blood:	n/a	n/a
23	POLR2A	chr15:52820828-52821633	GM10847	blood:	n/a	n/a
24	SIN3A	chr15:52819993-52822243	H1-hESC	embryonic stem cell:	n/a	chr15:52820934-52820945 chr15:52820710-52820721 chr15:52820874-52820887 chr15:52821085-52821096 chr15:52821567-52821578
25	MAZ	chr15:52820760-52821715	GM12878	blood:	n/a	chr15:52821025-52821035 chr15:52820897-52820907
26	GTF2F1	chr15:52821612-52821799	Hela-S3	cervix:	n/a	n/a
27	YY1	chr15:52820618-52821709	GM12878	blood:	n/a	chr15:52820959-52820968 chr15:52821454-52821468 chr15:52820735-52820746 chr15:52821085-52821096 chr15:52821460-52821474 chr15:52821465-52821474 chr15:52821457-52821471 chr15:52821462-52821471 chr15:52821462-52821473 chr15:52821086-52821100
28	MAX	chr15:52821214-52821688	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr15:52820722-52821660	ProgFib	skin:	n/a	n/a
30	RAD21	chr15:52821196-52821680	MCF-7	breast:	n/a	chr15:52821564-52821577
31	YY1	chr15:52821212-52821741	SK-N-SH_RA	brain:	n/a	chr15:52821454-52821468 chr15:52821460-52821474 chr15:52821465-52821474 chr15:52821457-52821471 chr15:52821462-52821471 chr15:52821462-52821473
32	YY1	chr15:52821172-52821711	HepG2	liver:	n/a	chr15:52821454-52821468 chr15:52821460-52821474 chr15:52821465-52821474 chr15:52821457-52821471 chr15:52821462-52821471 chr15:52821462-52821473
33	RAD21	chr15:52821194-52821684	A549	lung:	n/a	chr15:52821564-52821577
34	POLR2A	chr15:52820801-52821744	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:52820050-52822134	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr15:52820491-52821765	Raji	blood:	n/a	n/a
37	MAZ	chr15:52820146-52822008	IMR90	lung:	n/a	chr15:52821025-52821035 chr15:52820897-52820907
38	POLR2A	chr15:52820454-52821707	GM12892	blood:	n/a	n/a
39	TAF1	chr15:52820335-52822050	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr15:52820168-52821903	A549	lung:	n/a	chr15:52821025-52821035 chr15:52820897-52820907
41	MAX	chr15:52820839-52821744	GM12878	blood:	n/a	chr15:52821025-52821035 chr15:52820897-52820907
42	PAX5	chr15:52820685-52821659	GM12892	blood:	n/a	n/a
43	MXI1	chr15:52819779-52821960	IMR90	lung:	n/a	chr15:52821233-52821242
44	POLR2A	chr15:52820725-52821714	U87	brain:	n/a	n/a
45	BCLAF1	chr15:52820727-52821738	GM12878	blood:	n/a	chr15:52821698-52821707 chr15:52821465-52821478 chr15:52821464-52821473 chr15:52821087-52821100 chr15:52821458-52821471 chr15:52821341-52821354
46	RAD21	chr15:52820945-52821647	ECC-1	luminal epithelium:	n/a	chr15:52821175-52821188 chr15:52821564-52821577
47	SIN3AK20	chr15:52820073-52822421	MCF-7	breast:	n/a	n/a
48	MAX	chr15:52820758-52821642	H1-hESC	embryonic stem cell:	n/a	chr15:52821025-52821035 chr15:52820897-52820907
49	RCOR1	chr15:52820943-52821650	Hela-S3	cervix:	n/a	n/a
50	MAX	chr15:52820374-52821704	A549	lung:	n/a	chr15:52821025-52821035 chr15:52820897-52820907

No.	Distal block	Cell Line	Cell type
1	chr15:52816804..52818865-chr15:52821369..52824453,4	K562	blood:
2	chr15:52819283..52821980-chr16:88877332..88878840,2	MCF-7	breast:
3	chr15:52584393..52589074-chr15:52819513..52822265,5	MCF-7	breast:
4	chr15:52820217..52824623-chr15:52859000..52863588,7	MCF-7	breast:
5	chr15:52820950..52823000-chr15:52846878..52849661,2	MCF-7	breast:
6	chr15:52820917..52821847-chr17:56736116..56736779,3	MCF-7	breast:
7	chr15:52821243..52824156-chr15:52859754..52862350,2	MCF-7	breast:

Variant related genes	Relation type
MYO5A	TF binding region
ENSG00000128833	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000198931	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13329510	1.00[EUR][1000 genomes]
rs1693512	0.90[AFR][1000 genomes]
rs1693517	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693519	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724599	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724602	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222656	1.00[EUR][1000 genomes]
rs28417081	1.00[EUR][1000 genomes]
rs28417825	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483042	1.00[EUR][1000 genomes]
rs28556791	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570350	1.00[EUR][1000 genomes]
rs28581262	1.00[EUR][1000 genomes]
rs28589619	1.00[ASN][1000 genomes]
rs28663524	1.00[EUR][1000 genomes]
rs28665952	1.00[EUR][1000 genomes]
rs28673564	1.00[EUR][1000 genomes]
rs28682547	1.00[EUR][1000 genomes]
rs28687913	1.00[EUR][1000 genomes]
rs28699673	1.00[EUR][1000 genomes]
rs28701803	1.00[ASN][1000 genomes]
rs28729511	1.00[EUR][1000 genomes]
rs28814017	1.00[EUR][1000 genomes]
rs28840839	1.00[EUR][1000 genomes]
rs28876722	1.00[EUR][1000 genomes]
rs7168981	1.00[EUR][1000 genomes]
rs73412972	1.00[EUR][1000 genomes]
rs73412975	1.00[EUR][1000 genomes]
rs73414913	1.00[ASN][1000 genomes]
rs7342673	1.00[EUR][1000 genomes]
rs9920195	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3406407	chr15:52820185-52823033	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
5	esv3444715	chr15:52820360-52822458	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52818400-52822000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:52819400-52822000	Active TSS	Brain Anterior Caudate	brain
3	chr15:52819600-52822000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr15:52819600-52822000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr15:52819800-52822000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr15:52819800-52822000	Active TSS	Brain Angular Gyrus	brain
7	chr15:52819800-52822200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr15:52819800-52822200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:52819800-52822600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr15:52820000-52821800	Active TSS	Fetal Brain Female	brain
11	chr15:52820000-52822000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:52820000-52822000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:52820000-52822000	Active TSS	Right Atrium	heart
14	chr15:52820000-52822000	Active TSS	Right Ventricle	heart
15	chr15:52820000-52822200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr15:52820000-52822200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:52820000-52822400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:52820200-52821800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr15:52820200-52821800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:52820200-52821800	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr15:52820200-52821800	Active TSS	Brain Hippocampus Middle	brain
22	chr15:52820200-52821800	Active TSS	Gastric	stomach
23	chr15:52820200-52821800	Active TSS	A549	lung
24	chr15:52820200-52821800	Active TSS	NHDF-Ad	bronchial
25	chr15:52820200-52822000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:52820200-52822000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:52820200-52822000	Active TSS	Ovary	ovary
28	chr15:52820200-52822200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:52820200-52822200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr15:52820400-52821800	Active TSS	H1 Cell Line	embryonic stem cell
31	chr15:52820400-52821800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr15:52820400-52821800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:52820400-52821800	Active TSS	Primary T cells from cord blood	blood
34	chr15:52820400-52821800	Active TSS	Colon Smooth Muscle	Colon
35	chr15:52820400-52821800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr15:52820400-52822000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:52820400-52822000	Active TSS	Brain Cingulate Gyrus	brain
38	chr15:52820400-52822000	Active TSS	Left Ventricle	heart
39	chr15:52820400-52822200	Active TSS	Rectal Smooth Muscle	rectum
40	chr15:52820400-52822400	Active TSS	Aorta	Aorta
41	chr15:52820600-52821800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr15:52820600-52821800	Active TSS	Psoas Muscle	Psoas
43	chr15:52820600-52821800	Active TSS	Small Intestine	intestine
44	chr15:52820600-52822000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr15:52820600-52822000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:52820600-52822000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:52820800-52822000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr15:52820800-52822000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
49	chr15:52821000-52821800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:52821000-52821800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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