Variant report

Variant	rs11169294
Chromosome Location	chr12:50561998-50561999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr12:50560021-50562090	Hela-S3	cervix:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50496593..50501221-chr12:50560690..50564425,5	MCF-7	breast:
2	chr12:50477885..50480264-chr12:50559751..50562542,2	K562	blood:
3	chr12:50534374..50536702-chr12:50560898..50562585,2	MCF-7	breast:
4	chr12:50499334..50507442-chr12:50559441..50562987,11	K562	blood:
5	chr12:50561032..50562687-chr12:50794487..50796124,2	K562	blood:
6	chr12:50503967..50508677-chr12:50559559..50562905,8	MCF-7	breast:
7	chr12:50504059..50507401-chr12:50559290..50562708,7	K562	blood:
8	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
9	chr12:50418073..50421025-chr12:50559963..50562659,2	MCF-7	breast:
10	chr12:50560048..50562244-chr12:50793488..50796318,2	MCF-7	breast:
11	chr12:50561668..50564351-chr12:50565248..50567736,2	MCF-7	breast:
12	chr12:50477150..50481052-chr12:50559881..50562931,6	MCF-7	breast:
13	chr12:50503326..50508590-chr12:50559314..50563839,9	MCF-7	breast:
14	chr12:50481586..50483446-chr12:50561055..50562611,2	MCF-7	breast:
15	chr1:202778953..202781660-chr12:50561318..50563251,2	MCF-7	breast:
16	chr12:50144547..50147013-chr12:50560890..50562715,2	MCF-7	breast:
17	chr12:50560617..50562645-chr12:51025558..51027180,2	K562	blood:
18	chr12:50561156..50562922-chr12:50613932..50615830,2	K562	blood:

No data

Variant related genes	Relation type
CERS5	TF binding region
ENSG00000167588	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000207136	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000260021	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000228288	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1044370	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10747570	0.87[EUR][1000 genomes]
rs11169300	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11831413	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426261	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12815871	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12824125	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830386	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1862043	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178173	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358538	0.81[ASN][1000 genomes]
rs34573394	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35549836	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35998534	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4883481	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4883482	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56709084	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580729	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66768395	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7136570	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7294548	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7297421	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301566	0.81[ASN][1000 genomes]
rs7301649	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301740	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7302981	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7308356	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7967705	0.86[EUR][1000 genomes]
rs7967844	0.87[EUR][1000 genomes]
rs7972842	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs836179	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836180	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169294	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50559200-50562000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:50559400-50562000	Active TSS	HSMM	muscle
3	chr12:50559400-50562200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:50559600-50562000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:50559600-50562000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:50560000-50562000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:50560000-50562000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:50560000-50562000	Active TSS	Rectal Smooth Muscle	rectum
9	chr12:50560000-50562200	Active TSS	HepG2	liver
10	chr12:50560400-50562000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:50560600-50562000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:50560600-50562000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:50560600-50562000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:50561200-50562000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:50561200-50569800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:50561200-50570600	Weak transcription	Aorta	Aorta
17	chr12:50561400-50562000	Flanking Active TSS	Liver	Liver
18	chr12:50561400-50562000	Flanking Active TSS	Fetal Lung	lung
19	chr12:50561400-50562000	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr12:50561400-50562000	Flanking Active TSS	Dnd41	blood
21	chr12:50561400-50562000	Flanking Active TSS	NH-A	brain
22	chr12:50561600-50562000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr12:50561600-50562000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:50561600-50562200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:50561600-50562800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:50561600-50563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:50561600-50563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:50561600-50570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:50561600-50570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:50561600-50570800	Weak transcription	Esophagus	oesophagus
31	chr12:50561600-50570800	Weak transcription	Gastric	stomach
32	chr12:50561600-50570800	Weak transcription	Pancreas	Pancrea
33	chr12:50561600-50571200	Weak transcription	Lung	lung
34	chr12:50561600-50571200	Weak transcription	Right Ventricle	heart
35	chr12:50561600-50575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:50561800-50562000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:50561800-50562000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:50561800-50562000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr12:50561800-50562000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:50561800-50562000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:50561800-50562000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:50561800-50562000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:50561800-50562000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:50561800-50562000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:50561800-50562000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr12:50561800-50562000	Enhancers	Fetal Heart	heart
47	chr12:50561800-50562000	Enhancers	Fetal Intestine Large	intestine
48	chr12:50561800-50562000	Enhancers	Fetal Intestine Small	intestine
49	chr12:50561800-50562000	Enhancers	Fetal Stomach	stomach
50	chr12:50561800-50562000	Enhancers	Fetal Thymus	thymus

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