Variant report

Variant	rs1724602
Chromosome Location	chr15:52822050-52822051
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	chr15:52820010-52822087	H1-neurons	neurons:	n/a	n/a
2	TBP	chr15:52821956-52822154	HepG2	liver:	n/a	n/a
3	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
4	POLR2A	chr15:52820050-52822134	H1-neurons	neurons:	n/a	n/a
5	TAF1	chr15:52820335-52822050	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr15:52820073-52822421	MCF-7	breast:	n/a	n/a
7	POLR2A	chr15:52820348-52822315	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAZ	chr15:52821953-52822050	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:52821966-52822156	HepG2	liver:	n/a	n/a
10	TCF7L2	chr15:52821697-52822308	HepG2	liver:	n/a	n/a
11	ELF1	chr15:52820336-52822279	MCF-7	breast:	n/a	chr15:52820882-52820894 chr15:52821461-52821473 chr15:52821465-52821474 chr15:52821037-52821049
12	TCF7L2	chr15:52821960-52822356	MCF-7	breast:	n/a	n/a
13	MAX	chr15:52820180-52822361	MCF-7	breast:	n/a	chr15:52821025-52821035 chr15:52820897-52820907
14	REST	chr15:52819834-52822509	H1-neurons	neurons:	n/a	chr15:52821236-52821249
15	MXI1	chr15:52819875-52822056	SK-N-SH	brain:	n/a	chr15:52821233-52821242
16	TCF7L2	chr15:52821954-52822199	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52816804..52818865-chr15:52821369..52824453,4	K562	blood:
2	chr15:52584393..52589074-chr15:52819513..52822265,5	MCF-7	breast:
3	chr15:52820217..52824623-chr15:52859000..52863588,7	MCF-7	breast:
4	chr15:52820950..52823000-chr15:52846878..52849661,2	MCF-7	breast:
5	chr15:52821243..52824156-chr15:52859754..52862350,2	MCF-7	breast:

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

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10518683	0.85[GIH][hapmap]
rs13329278	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs13329500	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs13329510	1.00[EUR][1000 genomes]
rs1358085	0.86[AFR][1000 genomes]
rs1669870	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1669872	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1693509	0.81[MKK][hapmap]
rs1693512	0.80[AFR][1000 genomes]
rs1693516	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693517	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964903	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs16964928	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs16964944	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs16964952	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1724577	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1724599	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724600	1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724607	0.81[MKK][hapmap]
rs2222656	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs2414145	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2414164	1.00[CHD][hapmap]
rs2462845	0.81[MKK][hapmap]
rs2600903	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2600904	0.85[GIH][hapmap];1.00[MEX][hapmap]
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]
rs4774620	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs4774621	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs7163778	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs7166034	0.85[GIH][hapmap];1.00[MEX][hapmap]
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[GIH][hapmap];1.00[EUR][1000 genomes]
rs744501	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs8029846	1.00[CHD][hapmap]
rs9920195	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS 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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52819800-52822200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr15:52819800-52822200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr15:52819800-52822600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr15:52820000-52822200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:52820000-52822200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr15:52820000-52822400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52820200-52822200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:52820200-52822200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr15:52820400-52822200	Active TSS	Rectal Smooth Muscle	rectum
10	chr15:52820400-52822400	Active TSS	Aorta	Aorta
11	chr15:52821400-52822200	Flanking Active TSS	Dnd41	blood
12	chr15:52821400-52822400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr15:52821400-52822400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:52821400-52822400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:52821600-52822200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:52821600-52822200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:52821600-52822200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr15:52821600-52822200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr15:52821600-52822200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:52821600-52822200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:52821600-52822200	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr15:52821600-52822200	Active TSS	Fetal Brain Male	brain
23	chr15:52821600-52822200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
24	chr15:52821600-52822200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
25	chr15:52821600-52822200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
26	chr15:52821600-52822200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
27	chr15:52821600-52822200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr15:52821600-52822200	Flanking Active TSS	GM12878-XiMat	blood
29	chr15:52821600-52822200	Flanking Active TSS	Hela-S3	cervix
30	chr15:52821600-52822200	Flanking Active TSS	HMEC	breast
31	chr15:52821600-52822200	Flanking Active TSS	HUVEC	blood vessel
32	chr15:52821600-52822200	Flanking Active TSS	NHLF	lung
33	chr15:52821600-52822400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:52821600-52822400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:52821600-52822400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr15:52821600-52822400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr15:52821600-52822400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:52821600-52822400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:52821600-52822400	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr15:52821600-52822400	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr15:52821600-52822400	Bivalent/Poised TSS	Fetal Kidney	kidney
42	chr15:52821600-52822400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr15:52821600-52822400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr15:52821600-52822400	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr15:52821600-52822600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr15:52821800-52822200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr15:52821800-52822200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52821800-52822200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:52821800-52822200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
50	chr15:52821800-52822200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood

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