Variant report

Variant	rs3759797
Chromosome Location	chr15:41135156-41135157
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41135053-41135296	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41131767..41134219-chr15:41134403..41136032,2	MCF-7	breast:
2	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
3	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
4	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
5	chr15:41121981..41124134-chr15:41133402..41135573,2	MCF-7	breast:
6	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
7	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
8	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
9	chr15:40985736..40987452-chr15:41134754..41137017,2	MCF-7	breast:
10	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

No data

Variant related genes	Relation type
SPINT1	TF binding region
ENSG00000261183	TF binding region
ENSG00000245849	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000104140	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16971177	0.90[GIH][hapmap]
rs16971186	0.90[GIH][hapmap]
rs4924508	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs58107694	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582639	0.90[ASN][1000 genomes]
rs658752	0.85[TSI][hapmap]
rs661745	0.92[ASN][1000 genomes]
rs662236	0.86[ASN][1000 genomes]
rs676180	0.85[TSI][hapmap]
rs689594	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs690435	0.96[ASN][1000 genomes]
rs690467	0.92[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41107200-41135200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:41107600-41135200	Weak transcription	Esophagus	oesophagus
3	chr15:41108200-41135600	Weak transcription	Spleen	Spleen
4	chr15:41112000-41135800	Weak transcription	Right Atrium	heart
5	chr15:41120800-41135600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:41121600-41135200	Weak transcription	Colonic Mucosa	Colon
7	chr15:41121600-41135200	Weak transcription	Gastric	stomach
8	chr15:41121600-41135200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:41121800-41135200	Weak transcription	Stomach Mucosa	stomach
10	chr15:41123200-41135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:41124800-41135200	Weak transcription	Pancreas	Pancrea
12	chr15:41131200-41135400	Weak transcription	Lung	lung
13	chr15:41131200-41135600	Weak transcription	K562	blood
14	chr15:41131400-41135200	Weak transcription	Placenta	Placenta
15	chr15:41132600-41135200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:41133600-41135200	Weak transcription	Fetal Kidney	kidney
17	chr15:41134600-41135200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:41135000-41135200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr15:41135000-41135200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:41135000-41135200	Enhancers	Fetal Intestine Large	intestine
21	chr15:41135000-41135200	Enhancers	Fetal Intestine Small	intestine
22	chr15:41135000-41135200	Enhancers	HMEC	breast
23	chr15:41135000-41135800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr15:41135000-41135800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:41135000-41135800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr15:41135000-41135800	Flanking Active TSS	NHEK	skin

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