Variant report

Variant	rs16964728
Chromosome Location	chr15:52374466-52374467
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	RUNX3	chr15:52374409-52375292	GM12878	blood:	n/a	n/a
2	MTA3	chr15:52374384-52375677	GM12878	blood:	n/a	n/a
3	EBF1	chr15:52374465-52375633	GM12878	blood:	n/a	n/a
4	YY1	chr15:52374357-52374632	GM12878	blood:	n/a	chr15:52374447-52374457 chr15:52374448-52374456 chr15:52374447-52374469 chr15:52374450-52374458
5	YY1	chr15:52374300-52374659	GM12878	blood:	n/a	chr15:52374447-52374457 chr15:52374448-52374456 chr15:52374447-52374469 chr15:52374450-52374458
6	ZNF384	chr15:52374269-52375593	GM12878	blood:	n/a	n/a
7	YY1	chr15:52374311-52374625	GM12892	blood:	n/a	chr15:52374447-52374457 chr15:52374448-52374456 chr15:52374447-52374469 chr15:52374450-52374458

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52262830..52265268-chr15:52372078..52374982,4	MCF-7	breast:
2	chr15:52308069..52314807-chr15:52359242..52376066,34	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259178	TF binding region
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12439307	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12443497	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12902522	1.00[CEU][hapmap]
rs16964729	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17612326	0.86[AMR][1000 genomes]
rs2414129	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs60289856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732097	0.82[JPT][hapmap]
rs73400750	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73400751	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73400758	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73400779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs875804	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9672817	0.84[ASN][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	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1039841	chr15:52357448-52381377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	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
6	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52362800-52374600	Weak transcription	Small Intestine	intestine
2	chr15:52370800-52374600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr15:52370800-52376400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:52371200-52374800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:52371200-52376600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:52371400-52377400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:52371600-52378800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:52371800-52374600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:52372800-52377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:52373000-52377400	Weak transcription	NHEK	skin
11	chr15:52373200-52378800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:52373400-52374600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:52373400-52377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:52373400-52377400	Weak transcription	HMEC	breast
15	chr15:52374000-52375600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:52374000-52375800	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:52374000-52376200	Enhancers	Primary hematopoietic stem cells	blood
18	chr15:52374200-52374800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:52374400-52374600	Enhancers	Brain Anterior Caudate	brain
20	chr15:52374400-52374600	Enhancers	Pancreas	Pancrea
21	chr15:52374400-52374600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr15:52374400-52374800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr15:52374400-52374800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:52374400-52374800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:52374400-52374800	Enhancers	Esophagus	oesophagus
26	chr15:52374400-52375000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:52374400-52375000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:52374400-52375000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr15:52374400-52375000	Enhancers	Colonic Mucosa	Colon
30	chr15:52374400-52375000	Enhancers	Duodenum Mucosa	Duodenum
31	chr15:52374400-52375000	Enhancers	Fetal Muscle Leg	muscle
32	chr15:52374400-52375000	Enhancers	Fetal Thymus	thymus
33	chr15:52374400-52375000	Flanking Active TSS	GM12878-XiMat	blood
34	chr15:52374400-52375200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr15:52374400-52375400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr15:52374400-52375600	Enhancers	Primary B cells from cord blood	blood
37	chr15:52374400-52375600	Enhancers	Dnd41	blood
38	chr15:52374400-52375600	Enhancers	HSMM	muscle
39	chr15:52374400-52376000	Enhancers	HSMMtube	muscle
40	chr15:52374400-52376200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:52374400-52376400	Enhancers	Rectal Mucosa Donor 29	rectum

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