Variant report

Variant	rs2694917
Chromosome Location	chr12:56912864-56912865
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	SP1	chr12:56912241-56912867	A549	lung:	n/a	n/a
2	TEAD4	chr12:56911565-56912976	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr12:56911531-56913125	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr12:56911576-56912955	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr12:56911321-56913121	ECC-1	luminal epithelium:	n/a	chr12:56912550-56912560
6	TCF12	chr12:56911556-56912991	ECC-1	luminal epithelium:	n/a	n/a
7	FOXM1	chr12:56911533-56913028	ECC-1	luminal epithelium:	n/a	n/a
8	NFIC	chr12:56911544-56912946	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr12:56911583-56913119	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr12:56912152-56912894	A549	lung:	n/a	chr12:56912550-56912560
11	TCF12	chr12:56912248-56912904	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56909353..56913090-chr12:57029717..57032466,3	K562	blood:

Variant related genes	Relation type
RBMS2	TF binding region
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1043011	0.82[JPT][hapmap]
rs12232026	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2638287	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638315	0.82[JPT][hapmap]
rs2657879	0.82[JPT][hapmap]
rs2657880	0.82[JPT][hapmap]
rs2657896	0.82[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs2657907	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2694919	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2933235	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3759091	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7302925	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs7304944	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs774211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs774213	0.88[AMR][1000 genomes]
rs774215	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs799260	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs799261	0.88[AMR][1000 genomes]
rs813497	0.84[JPT][hapmap];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite ratios	24816252	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2694917	SPRYD4	cis	multi-tissue	Pritchard
rs2694917	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56911000-56913200	Enhancers	HMEC	breast
2	chr12:56911600-56913200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:56911600-56915200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:56911600-56915200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:56911800-56913200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:56911800-56913200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:56911800-56913200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:56911800-56913200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:56911800-56914000	Enhancers	HUVEC	blood vessel
10	chr12:56911800-56914800	Enhancers	Osteobl	bone
11	chr12:56911800-56915200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:56911800-56915200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:56912000-56913000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr12:56912000-56913000	Enhancers	NHDF-Ad	bronchial
15	chr12:56912000-56914800	Weak transcription	Fetal Thymus	thymus
16	chr12:56912200-56913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:56912200-56913800	Enhancers	Adipose Nuclei	Adipose
18	chr12:56912200-56915800	Weak transcription	Gastric	stomach
19	chr12:56912200-56915800	Weak transcription	Lung	lung
20	chr12:56912400-56913000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:56912400-56913000	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:56912400-56914000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:56912600-56913200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:56912600-56913800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:56912600-56913800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:56912600-56913800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:56912600-56913800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:56912600-56913800	Weak transcription	NHLF	lung
29	chr12:56912600-56914000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:56912600-56914000	Weak transcription	Primary B cells from cord blood	blood
31	chr12:56912600-56914000	Enhancers	Hela-S3	cervix
32	chr12:56912600-56914000	Weak transcription	HepG2	liver
33	chr12:56912600-56914000	Weak transcription	HSMMtube	muscle
34	chr12:56912600-56914000	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr12:56912600-56914200	Enhancers	Fetal Muscle Leg	muscle
36	chr12:56912600-56915200	Enhancers	NHEK	skin
37	chr12:56912800-56913200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:56912800-56913800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:56912800-56913800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:56912800-56913800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:56912800-56913800	Weak transcription	Fetal Lung	lung
42	chr12:56912800-56913800	Weak transcription	HSMM	muscle
43	chr12:56912800-56914000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:56912800-56914000	Enhancers	A549	lung
45	chr12:56912800-56914200	Weak transcription	Colonic Mucosa	Colon
46	chr12:56912800-56914400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:56912800-56914600	Weak transcription	NH-A	brain
48	chr12:56912800-56915600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:56912800-56917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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