Variant report

Variant	rs3759796
Chromosome Location	chr15:41055195-41055196
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	MAX	chr15:41055194-41056853	HepG2	liver:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
2	MAX	chr15:41055186-41057114	ECC-1	luminal epithelium:	n/a	chr15:41056062-41056072 chr15:41055747-41055757
3	NRF1	chr15:41055173-41055832	SK-N-SH	brain:	n/a	chr15:41055501-41055512 chr15:41055501-41055515 chr15:41055501-41055512 chr15:41055498-41055512
4	POLR2A	chr15:41055079-41057215	HepG2	liver:	n/a	n/a
5	HCFC1	chr15:41054658-41062813	Hela-S3	cervix:	n/a	n/a
6	NFIC	chr15:41055178-41057077	ECC-1	luminal epithelium:	n/a	chr15:41055583-41055599 chr15:41055582-41055599 chr15:41055581-41055598

No.	Distal block	Cell Line	Cell type
1	chr15:41053870..41057648-chr15:41097391..41099914,3	K562	blood:
2	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
3	chr15:41047499..41049695-chr15:41052688..41055612,2	MCF-7	breast:
4	chr15:41054213..41057951-chr15:41097645..41100150,5	K562	blood:
5	chr15:41053928..41056375-chr15:41057436..41059478,2	MCF-7	breast:
6	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:
7	chr15:41036948..41038953-chr15:41054723..41057087,2	K562	blood:

Variant related genes	Relation type
GCHFR	TF binding region
ENSG00000188277	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11070290	0.85[EUR][1000 genomes]
rs11855641	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12898552	0.84[EUR][1000 genomes]
rs12910784	0.85[EUR][1000 genomes]
rs2010300	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289219	0.93[EUR][1000 genomes]
rs2304583	0.86[EUR][1000 genomes]
rs2412545	0.83[EUR][1000 genomes]
rs2899000	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34621344	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34988257	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45592734	0.83[EUR][1000 genomes]
rs5030783	0.82[EUR][1000 genomes]
rs62018584	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8031427	0.83[EUR][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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3759796	C15orf57	cis	Muscle Skeletal	GTEx
rs3759796	C15orf57	cis	Nerve Tibial	GTEx
rs3759796	C15orf57	cis	Artery Tibial	GTEx
rs3759796	RP11-111A22.1	cis	Stomach	GTEx
rs3759796	C15orf57	cis	Stomach	GTEx
rs3759796	C15orf57	cis	Esophagus Mucosa	GTEx
rs3759796	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs3759796	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs3759796	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs3759796	C15orf57	cis	Adipose Subcutaneous	GTEx
rs3759796	C15orf57	cis	lung	GTEx
rs3759796	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs3759796	RP11-111A22.1	cis	lung	GTEx
rs3759796	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs3759796	DISP2	cis	Thyroid	GTEx
rs3759796	C15orf57	cis	Esophagus Muscularis	GTEx
rs3759796	RP11-111A22.1	cis	Artery Tibial	GTEx
rs3759796	C15orf57	cis	Artery Aorta	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41048000-41055200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41048000-41055200	Weak transcription	Brain Substantia Nigra	brain
3	chr15:41048000-41055200	Weak transcription	NH-A	brain
4	chr15:41048000-41055400	Weak transcription	Brain Angular Gyrus	brain
5	chr15:41048000-41055400	Weak transcription	Right Atrium	heart
6	chr15:41048200-41055200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:41048200-41055200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:41048200-41055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:41048200-41055400	Weak transcription	Liver	Liver
10	chr15:41048200-41055400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:41048200-41055400	Weak transcription	A549	lung
12	chr15:41048400-41055200	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:41048400-41055400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:41049200-41055200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:41049200-41055400	Weak transcription	GM12878-XiMat	blood
16	chr15:41049800-41055400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:41053000-41055600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:41053200-41055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:41053200-41055400	Weak transcription	Thymus	Thymus
20	chr15:41054400-41055400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:41054400-41055400	Enhancers	Fetal Intestine Small	intestine
22	chr15:41054400-41055600	Enhancers	Primary hematopoietic stem cells	blood
23	chr15:41054600-41055200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41054600-41055200	Enhancers	Placenta	Placenta
25	chr15:41054600-41055400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:41054600-41055400	Enhancers	Fetal Intestine Large	intestine
27	chr15:41054600-41055400	Enhancers	Fetal Stomach	stomach
28	chr15:41054600-41055400	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr15:41054800-41055200	Enhancers	Primary T cells from cord blood	blood
30	chr15:41054800-41055200	Enhancers	Hela-S3	cervix
31	chr15:41054800-41055200	Enhancers	HepG2	liver
32	chr15:41054800-41055200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr15:41054800-41055400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:41054800-41055400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:41054800-41055400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:41054800-41055400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr15:41054800-41055400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:41054800-41055400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:41054800-41055400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:41054800-41055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:41054800-41055400	Bivalent Enhancer	Brain Germinal Matrix	brain
42	chr15:41054800-41055400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr15:41054800-41055400	Enhancers	Fetal Lung	lung
44	chr15:41054800-41055400	Enhancers	Fetal Muscle Leg	muscle
45	chr15:41054800-41055400	Enhancers	Stomach Mucosa	stomach
46	chr15:41054800-41055400	Enhancers	HUVEC	blood vessel
47	chr15:41054800-41055400	Enhancers	K562	blood
48	chr15:41054800-41056600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:41055000-41055200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr15:41055000-41055200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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