Variant report

Variant	rs2694919
Chromosome Location	chr12:56917390-56917391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56916521..56918137-chr12:56919957..56922129,2	MCF-7	breast:
2	chr12:56916433..56918956-chr12:56923495..56926214,2	MCF-7	breast:
3	chr12:56916195..56918397-chr12:57055172..57057323,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2638287	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638301	0.89[AMR][1000 genomes]
rs2657896	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2657907	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694917	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2933235	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774211	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774213	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs774215	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs799260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs799261	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs813497	1.00[AMR][1000 genomes];0.97[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2694919	SPRYD4	cis	multi-tissue	Pritchard
rs2694919	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56914000-56917400	Active TSS	Right Atrium	heart
2	chr12:56914000-56917400	Active TSS	Right Ventricle	heart
3	chr12:56914000-56918400	Active TSS	Stomach Smooth Muscle	stomach
4	chr12:56914000-56919200	Weak transcription	Spleen	Spleen
5	chr12:56914400-56918600	Active TSS	NHLF	lung
6	chr12:56915000-56917600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:56915000-56917600	Active TSS	NHDF-Ad	bronchial
8	chr12:56915000-56918600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:56915000-56918600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:56915200-56917400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:56915200-56917400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:56915200-56917800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:56915200-56918000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:56915200-56918400	Active TSS	HMEC	breast
15	chr12:56915200-56918800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:56915200-56919000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:56915400-56917400	Active TSS	Fetal Stomach	stomach
18	chr12:56915400-56917800	Active TSS	A549	lung
19	chr12:56915400-56917800	Active TSS	Hela-S3	cervix
20	chr12:56915400-56918000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:56915400-56918000	Active TSS	NHEK	skin
22	chr12:56915400-56918200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:56915400-56918200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:56915400-56918400	Active TSS	HSMM	muscle
25	chr12:56915600-56917800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr12:56915600-56917800	Active TSS	NH-A	brain
27	chr12:56915600-56918600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:56915800-56917600	Active TSS	Lung	lung
29	chr12:56916200-56917600	Flanking Active TSS	Fetal Kidney	kidney
30	chr12:56916400-56918200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:56916400-56918800	Flanking Active TSS	HUVEC	blood vessel
32	chr12:56916600-56917600	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr12:56916600-56918200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:56916600-56918600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr12:56916600-56923200	Weak transcription	Small Intestine	intestine
36	chr12:56916800-56917600	Active TSS	Fetal Muscle Leg	muscle
37	chr12:56916800-56918000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:56916800-56918000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:56916800-56918200	Flanking Active TSS	Osteobl	bone
40	chr12:56916800-56918400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:56916800-56918400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:56916800-56920200	Weak transcription	HepG2	liver
43	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:56917000-56917400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:56917000-56917400	Enhancers	Fetal Thymus	thymus
46	chr12:56917000-56917400	Enhancers	Left Ventricle	heart
47	chr12:56917000-56917400	Enhancers	Dnd41	blood
48	chr12:56917000-56917400	Flanking Active TSS	HSMMtube	muscle
49	chr12:56917000-56917600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:56917000-56917600	Enhancers	Brain Germinal Matrix	brain

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