Variant report

Variant	rs9972363
Chromosome Location	chr15:40748718-40748719
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	MYC	chr15:40748399-40749147	MCF10A-Er-Src	breast:	n/a	chr15:40748667-40748676 chr15:40748667-40748677 chr15:40748667-40748676 chr15:40748668-40748675
2	MAX	chr15:40748628-40748782	Hela-S3	cervix:	n/a	chr15:40748667-40748676 chr15:40748667-40748677 chr15:40748667-40748676 chr15:40748668-40748675
3	FOS	chr15:40748525-40748941	MCF10A-Er-Src	breast:	n/a	chr15:40748780-40748792
4	GATA3	chr15:40748452-40748804	T-47D	breast:	n/a	chr15:40748607-40748615
5	FOS	chr15:40748484-40748819	MCF10A-Er-Src	breast:	n/a	chr15:40748780-40748792
6	MYC	chr15:40748453-40749144	MCF10A-Er-Src	breast:	n/a	chr15:40748667-40748676 chr15:40748667-40748677 chr15:40748667-40748676 chr15:40748668-40748675
7	FOS	chr15:40748525-40748815	MCF10A-Er-Src	breast:	n/a	chr15:40748780-40748792
8	STAT3	chr15:40748451-40748991	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr15:40748590-40748805	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr15:40748616-40748723	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr15:40748597-40748960	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr15:40748558-40748795	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr15:40748674-40748868	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40729975..40738939-chr15:40745780..40750666,13	K562	blood:
2	chr15:40737690..40739438-chr15:40747846..40750336,2	MCF-7	breast:

Variant related genes	Relation type
BAHD1	TF binding region
ENSG00000259364	TF binding region
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10851396	0.88[MEX][hapmap]
rs11070279	0.88[MEX][hapmap]
rs11853333	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs11857247	0.81[MEX][hapmap]
rs12898690	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908114	0.88[MEX][hapmap]
rs1453183	0.88[MEX][hapmap]
rs731640	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs733299	0.81[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs8025458	0.88[MEX][hapmap]
rs9672313	0.82[GIH][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs9972363	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs9972363	CCDC32	cis	normal skin	skin_eQTL
rs9972363	C15orf57	cis	Cerebellum	GTEx
rs9972363	C15orf23	cis	parietal	SCAN
rs9972363	LPCAT4	cis	parietal	SCAN
rs9972363	ZFYVE19	cis	parietal	SCAN
rs9972363	KNSTRN	cis	Heart Left Ventricle	GTEx
rs9972363	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs9972363	C15orf57	cis	cerebellum	SCAN
rs9972363	C15orf57	cis	Adipose Subcutaneous	GTEx
rs9972363	C15orf23	cis	cerebellum	SCAN
rs9972363	C15orf57	cis	lung	GTEx
rs9972363	C15orf57	cis	Artery Tibial	GTEx
rs9972363	RP11-111A22.1	cis	Stomach	GTEx
rs9972363	C15orf57	cis	Esophagus Mucosa	GTEx
rs9972363	ZFYVE19	cis	cerebellum	SCAN
rs9972363	C15orf57	cis	Esophagus Muscularis	GTEx
rs9972363	PLA2G4E	cis	parietal	SCAN
rs9972363	C15orf57	cis	lymphoblastoid	seeQTL
rs9972363	C15orf57	cis	parietal	SCAN
rs9972363	RP11-111A22.1	cis	lung	GTEx
rs9972363	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs9972363	RP11-111A22.1	cis	Artery Tibial	GTEx
rs9972363	CCDC32	cis	multi-tissue	Pritchard
rs9972363	IVD	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40734800-40751000	Weak transcription	Aorta	Aorta
2	chr15:40738000-40750400	Weak transcription	Brain Germinal Matrix	brain
3	chr15:40738200-40751000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:40740600-40749600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr15:40742200-40749200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr15:40742200-40749600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:40742400-40762200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:40742600-40749400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr15:40742600-40750000	Enhancers	Fetal Intestine Large	intestine
10	chr15:40742800-40749600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:40742800-40750000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:40743400-40749200	Enhancers	Fetal Thymus	thymus
13	chr15:40743600-40749400	Enhancers	Spleen	Spleen
14	chr15:40744000-40750000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:40744200-40756400	Weak transcription	Fetal Kidney	kidney
16	chr15:40744400-40749000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:40744400-40749200	Enhancers	Small Intestine	intestine
18	chr15:40744600-40749600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:40744800-40749800	Enhancers	HepG2	liver
20	chr15:40745000-40749200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr15:40745000-40751000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr15:40745200-40750400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:40745600-40749000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:40745600-40751000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:40745800-40750600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:40745800-40751000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:40745800-40751200	Weak transcription	Liver	Liver
28	chr15:40746000-40749200	Enhancers	Brain Hippocampus Middle	brain
29	chr15:40746000-40749400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:40746000-40749400	Enhancers	Left Ventricle	heart
31	chr15:40746000-40749400	Enhancers	Pancreas	Pancrea
32	chr15:40746000-40749600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:40746000-40749800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:40746000-40750000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr15:40746200-40748800	Enhancers	Colonic Mucosa	Colon
36	chr15:40746200-40749000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:40746200-40749200	Enhancers	Stomach Mucosa	stomach
38	chr15:40746200-40749400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr15:40746200-40749400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr15:40746200-40749600	Enhancers	Fetal Muscle Trunk	muscle
41	chr15:40746200-40749800	Enhancers	Placenta	Placenta
42	chr15:40746400-40749000	Enhancers	HSMMtube	muscle
43	chr15:40746400-40749400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:40746400-40749400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:40746400-40749400	Enhancers	Lung	lung
46	chr15:40746400-40749400	Enhancers	Right Atrium	heart
47	chr15:40746400-40749400	Enhancers	Right Ventricle	heart
48	chr15:40746600-40749000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:40746600-40749000	Enhancers	HSMM	muscle
50	chr15:40746600-40749200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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