Variant report

Variant	rs73402816
Chromosome Location	chr15:52397021-52397022
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	SP1	chr15:52396748-52397302	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:52396551-52397192	GM12878	blood:	n/a	n/a
3	PAX5	chr15:52396965-52397186	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:52395596-52397248	GM12878	blood:	n/a	n/a
5	TBP	chr15:52396727-52397237	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:52396599-52397126	GM12878	blood:	n/a	n/a
7	POU2F2	chr15:52396842-52397221	GM12891	blood:	n/a	chr15:52397074-52397084 chr15:52397075-52397083
8	BHLHE40	chr15:52396632-52397277	GM12878	blood:	n/a	n/a
9	MAZ	chr15:52396899-52397262	GM12878	blood:	n/a	n/a
10	POU2F2	chr15:52396811-52397202	GM12878	blood:	n/a	chr15:52397074-52397084 chr15:52397075-52397083
11	POLR2A	chr15:52396491-52397148	GM12892	blood:	n/a	n/a
12	EBF1	chr15:52396615-52397249	GM12878	blood:	n/a	chr15:52396834-52396845
13	MTA3	chr15:52396364-52397381	GM12878	blood:	n/a	n/a
14	CTCF	chr15:52397020-52397170	GM12873	blood:	n/a	n/a
15	PAX5	chr15:52396671-52397223	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:52396708-52397132	GM12892	blood:	n/a	n/a
17	CTCF	chr15:52397020-52397170	GM12878	blood:	n/a	n/a
18	CTCF	chr15:52397000-52397150	GM12866	blood:	n/a	n/a
19	CTCF	chr15:52397020-52397170	GM12871	blood:	n/a	n/a
20	MAX	chr15:52396809-52397194	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:52395490-52397230	GM12878	blood:	n/a	n/a
22	ATF2	chr15:52396615-52397324	GM12878	blood:	n/a	n/a
23	POLR2A	chr15:52396501-52397168	GM12891	blood:	n/a	n/a
24	POLR2A	chr15:52396433-52397145	GM12891	blood:	n/a	n/a
25	WRNIP1	chr15:52396621-52397184	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:52395399-52397274	GM12878	blood:	n/a	n/a
27	SMC3	chr15:52396776-52397241	GM12878	blood:	n/a	n/a
28	RUNX3	chr15:52396518-52397304	GM12878	blood:	n/a	n/a
29	CTCF	chr15:52397001-52397156	GM19238	blood:	n/a	n/a
30	CTCF	chr15:52397020-52397170	GM12875	blood:	n/a	n/a
31	PML	chr15:52396479-52397239	GM12878	blood:	n/a	n/a
32	MTA3	chr15:52396604-52397171	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:52396580-52397163	GM12878	blood:	n/a	n/a
34	ZNF384	chr15:52396882-52397350	GM12878	blood:	n/a	n/a
35	EP300	chr15:52396687-52397284	GM12878	blood:	n/a	chr15:52397194-52397208
36	POLR2A	chr15:52396651-52397227	GM12891	blood:	n/a	n/a
37	CTCF	chr15:52396907-52397285	GM12878	blood:	n/a	n/a
38	FOXM1	chr15:52396611-52397137	GM12878	blood:	n/a	n/a
39	YY1	chr15:52396910-52397190	GM12878	blood:	n/a	n/a
40	CHD2	chr15:52396590-52397263	GM12878	blood:	n/a	n/a
41	ZNF143	chr15:52396981-52397190	GM12878	blood:	n/a	n/a
42	CTCF	chr15:52397015-52397150	GM12892	blood:	n/a	n/a
43	POU2F2	chr15:52396408-52397266	GM12878	blood:	n/a	chr15:52397074-52397084 chr15:52397075-52397083
44	POLR2A	chr15:52396482-52397274	GM12892	blood:	n/a	n/a
45	EBF1	chr15:52396614-52397176	GM12878	blood:	n/a	chr15:52396834-52396845
46	POLR2A	chr15:52396442-52397284	GM12892	blood:	n/a	n/a
47	CTCF	chr15:52397020-52397170	GM06990	blood:	n/a	n/a
48	POLR2A	chr15:52396702-52397100	GM12878	blood:	n/a	n/a
49	POU2F2	chr15:52396900-52397133	GM12878	blood:	n/a	chr15:52397074-52397084 chr15:52397075-52397083
50	RUNX3	chr15:52396533-52397319	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52385306..52387666-chr15:52394870..52397367,3	MCF-7	breast:
2	chr15:52395553..52398772-chr15:52399645..52403144,6	MCF-7	breast:
3	chr15:52394818..52397658-chr15:52475516..52477095,2	MCF-7	breast:
4	chr15:52389305..52392233-chr15:52393391..52397295,3	K562	blood:

Variant related genes	Relation type
ENSG00000259712	TF binding region
ENSG00000242327	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs60397096	0.96[AFR][1000 genomes];1.00[AMR][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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52386200-52399000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52392200-52400800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:52392400-52398600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:52392600-52398600	Enhancers	HMEC	breast
5	chr15:52392600-52398600	Enhancers	NHEK	skin
6	chr15:52393000-52397200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:52393200-52401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:52393200-52401800	Weak transcription	Pancreas	Pancrea
9	chr15:52393400-52398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:52394000-52397800	Enhancers	Primary B cells from peripheral blood	blood
11	chr15:52394200-52397400	Enhancers	Primary B cells from cord blood	blood
12	chr15:52395200-52398000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:52395800-52397200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:52395800-52398000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:52395800-52398200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:52395800-52401200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:52396000-52397800	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:52396000-52398000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:52396000-52401000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:52396000-52401800	Weak transcription	HSMM	muscle
21	chr15:52396200-52398000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:52396800-52397800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:52396800-52399000	Weak transcription	Spleen	Spleen
24	chr15:52396800-52401000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:52397000-52398000	Weak transcription	HepG2	liver
26	chr15:52397000-52398200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:52397000-52398800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:52397000-52398800	Weak transcription	Hela-S3	cervix
29	chr15:52397000-52399000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:52397000-52401000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:52397000-52401000	Weak transcription	Adipose Nuclei	Adipose
32	chr15:52397000-52401000	Enhancers	GM12878-XiMat	blood

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