Variant report

Variant	rs28707327
Chromosome Location	chr15:41163107-41163108
allele	G/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	chr15:41162871-41163185	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:41162983-41163263	GM12878	blood:	n/a	n/a
3	PML	chr15:41162539-41163353	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:41162051-41163344	GM12878	blood:	n/a	n/a
5	PAX5	chr15:41162767-41163266	GM12878	blood:	n/a	chr15:41162940-41162949
6	TCF3	chr15:41162884-41163340	GM12878	blood:	n/a	chr15:41163189-41163198 chr15:41163186-41163201
7	POLR2A	chr15:41162692-41163306	GM12891	blood:	n/a	n/a
8	TCF12	chr15:41162719-41163254	GM12878	blood:	n/a	chr15:41163199-41163206
9	POLR2A	chr15:41162698-41163310	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:41162930-41163136	GM12891	blood:	n/a	n/a
11	POLR2A	chr15:41161732-41164784	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr15:41162620-41163346	GM12892	blood:	n/a	n/a
13	MTA3	chr15:41162490-41163322	GM12878	blood:	n/a	n/a
14	ATF2	chr15:41162726-41163235	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:41161738-41164928	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:41163096-41163317	MCF-7	breast:	n/a	n/a
17	POU2F2	chr15:41162888-41163199	GM12878	blood:	n/a	n/a
18	STAT5A	chr15:41162656-41163266	GM12878	blood:	n/a	chr15:41163214-41163222 chr15:41162937-41162949
19	NFIC	chr15:41162700-41163243	GM12878	blood:	n/a	n/a
20	RUNX3	chr15:41162845-41163238	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:41162820-41166815	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr15:41162950-41163280	GM12878	blood:	n/a	chr15:41163199-41163206
23	EBF1	chr15:41162857-41163274	GM12878	blood:	n/a	chr15:41162915-41162926
24	POLR2A	chr15:41162585-41163352	GM12892	blood:	n/a	n/a
25	TCF3	chr15:41162967-41163304	GM12878	blood:	n/a	chr15:41163189-41163198 chr15:41163186-41163201
26	MYC	chr15:41162916-41163121	MCF10A-Er-Src	breast:	n/a	n/a
27	ZEB1	chr15:41162882-41163273	GM12878	blood:	n/a	n/a
28	MTA3	chr15:41162931-41163254	GM12878	blood:	n/a	n/a
29	WRNIP1	chr15:41162809-41163134	GM12878	blood:	n/a	n/a
30	NFATC1	chr15:41162752-41163269	GM12878	blood:	n/a	n/a
31	CTCF	chr15:41163086-41163130	GM19239	blood:	n/a	n/a
32	FOXM1	chr15:41162803-41163201	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:41162934-41165022	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:41162172-41166666	GM12878	blood:	n/a	n/a
35	POU2F2	chr15:41162570-41163306	GM12878	blood:	n/a	chr15:41162580-41162592
36	POLR2A	chr15:41161854-41166680	GM12878	blood:	n/a	n/a
37	EBF1	chr15:41162677-41163233	GM12878	blood:	n/a	chr15:41162915-41162926
38	POLR2A	chr15:41162962-41163274	GM12891	blood:	n/a	n/a
39	POLR2A	chr15:41163052-41163152	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
2	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
3	chr15:41116410..41118480-chr15:41162646..41165359,2	MCF-7	breast:
4	chr15:41161907..41163827-chr15:41163924..41166003,2	K562	blood:
5	chr15:41161359..41163442-chr15:41220401..41223293,2	K562	blood:
6	chr15:41162038..41163598-chr15:41167712..41169410,2	K562	blood:
7	chr15:41162876..41167684-chr15:41196844..41200482,5	MCF-7	breast:
8	chr15:41160986..41163743-chr15:41163845..41166495,2	K562	blood:
9	chr15:41161115..41163324-chr15:41164586..41166568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264256	TF binding region
ENSG00000104140	Chromatin interaction
ENSG00000128917	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000166145	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16971115	0.84[AFR][1000 genomes]
rs7179443	0.85[AMR][1000 genomes]
rs8028214	0.85[AMR][1000 genomes]
rs8042308	0.98[AFR][1000 genomes]
rs9744921	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
2	chr15:41150000-41165600	Weak transcription	Spleen	Spleen
3	chr15:41151600-41165400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:41152000-41163800	Weak transcription	Gastric	stomach
5	chr15:41156200-41164000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:41156600-41163600	Weak transcription	Fetal Intestine Small	intestine
7	chr15:41158600-41163600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41158600-41163800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:41158600-41163800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:41158600-41163800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:41158600-41163800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:41158800-41163800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:41158800-41164000	Weak transcription	A549	lung
14	chr15:41159000-41163400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:41159000-41163800	Weak transcription	HMEC	breast
16	chr15:41161800-41163800	Enhancers	Pancreas	Pancrea
17	chr15:41161800-41164200	Enhancers	Placenta	Placenta
18	chr15:41162000-41164000	Weak transcription	Colonic Mucosa	Colon
19	chr15:41162400-41163600	Enhancers	GM12878-XiMat	blood
20	chr15:41162600-41163200	Enhancers	Adipose Nuclei	Adipose
21	chr15:41162600-41163200	Flanking Active TSS	Hela-S3	cervix
22	chr15:41162600-41163800	Weak transcription	Esophagus	oesophagus
23	chr15:41162600-41165000	Enhancers	Stomach Mucosa	stomach
24	chr15:41163000-41163200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:41163000-41163800	Weak transcription	Small Intestine	intestine
26	chr15:41163000-41165800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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