Variant report

Variant	rs934935
Chromosome Location	chr15:40635177-40635178
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	MAZ	chr15:40635062-40637277	IMR90	lung:	n/a	n/a
2	CTCF	chr15:40635143-40637481	SK-N-SH	brain:	n/a	chr15:40636926-40636947 chr15:40636924-40636942 chr15:40637299-40637312 chr15:40637257-40637266
3	FOXA1	chr15:40634801-40635234	T-47D	breast:	n/a	n/a
4	STAT3	chr15:40634709-40635177	MCF10A-Er-Src	breast:	n/a	chr15:40635118-40635129
5	POLR2A	chr15:40635067-40637109	IMR90	lung:	n/a	n/a
6	POLR2A	chr15:40635145-40635411	HUVEC	blood vessel:	n/a	n/a
7	RCOR1	chr15:40634368-40637165	IMR90	lung:	n/a	n/a
8	EP300	chr15:40634703-40635283	T-47D	breast:	n/a	n/a
9	POLR2A	chr15:40635061-40637089	U87	brain:	n/a	n/a
10	FOS	chr15:40634672-40636307	HUVEC	blood vessel:	n/a	chr15:40635890-40635901 chr15:40635888-40635899 chr15:40635772-40635786
11	RFX5	chr15:40634386-40637249	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40632962..40635385-chr15:40697134..40699617,2	MCF-7	breast:

Variant related genes	Relation type
C15orf52	TF binding region
ENSG00000128928	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12440659	0.86[JPT][hapmap]
rs2004251	0.86[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2118960	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412511	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs934935	NDUFAF1	cis	cerebellum	SCAN
rs934935	PLA2G4E	cis	parietal	SCAN
rs934935	JMJD7-PLA2G4B	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
2	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
3	chr15:40629400-40637200	Enhancers	Fetal Lung	lung
4	chr15:40630400-40635400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:40630600-40636600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:40632200-40635200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:40632800-40637000	Weak transcription	Fetal Thymus	thymus
8	chr15:40633000-40636400	Enhancers	Right Atrium	heart
9	chr15:40633000-40637200	Enhancers	Fetal Muscle Leg	muscle
10	chr15:40633000-40637400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:40633000-40637400	Enhancers	NHDF-Ad	bronchial
12	chr15:40633000-40638800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:40633000-40640600	Enhancers	Fetal Intestine Small	intestine
14	chr15:40633200-40635800	Enhancers	Left Ventricle	heart
15	chr15:40633200-40637400	Enhancers	Right Ventricle	heart
16	chr15:40633200-40637400	Enhancers	HMEC	breast
17	chr15:40633200-40637400	Enhancers	NHEK	skin
18	chr15:40633200-40637400	Enhancers	NHLF	lung
19	chr15:40633200-40637600	Enhancers	HUVEC	blood vessel
20	chr15:40633200-40639400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:40633200-40641600	Enhancers	Esophagus	oesophagus
22	chr15:40633400-40635800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:40633400-40636600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:40633400-40636600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:40633400-40637000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr15:40633400-40637000	Weak transcription	Small Intestine	intestine
27	chr15:40633400-40637200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:40633400-40637800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:40633600-40635200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:40633600-40635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:40633600-40635200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:40633600-40635200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:40633600-40635200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:40633600-40635200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:40633600-40635200	Weak transcription	Placenta	Placenta
36	chr15:40633600-40635200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr15:40633600-40635200	Enhancers	Rectal Smooth Muscle	rectum
38	chr15:40633600-40635400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:40633600-40635400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:40633600-40635800	Enhancers	Stomach Smooth Muscle	stomach
41	chr15:40633600-40636600	Weak transcription	Ovary	ovary
42	chr15:40633600-40636600	Weak transcription	Pancreas	Pancrea
43	chr15:40633600-40637200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:40633600-40637200	Enhancers	Osteobl	bone
45	chr15:40633600-40642800	Enhancers	Stomach Mucosa	stomach
46	chr15:40633600-40644800	Weak transcription	Brain Germinal Matrix	brain
47	chr15:40633600-40645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:40633800-40635200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:40633800-40635200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:40633800-40635200	Weak transcription	Brain Hippocampus Middle	brain

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