Variant report

Variant	rs12967249
Chromosome Location	chr18:12949600-12949601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12881395..12884200-chr18:12946697..12949759,6	MCF-7	breast:
2	chr18:12948345..12951130-chr18:12969418..12973863,3	K562	blood:
3	chr18:12726304..12729223-chr18:12948825..12951791,2	K562	blood:
4	chr18:12880282..12884361-chr18:12946145..12949673,9	K562	blood:
5	chr18:12946883..12949783-chr18:12990489..12993346,5	MCF-7	breast:
6	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
7	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
8	chr18:12700812..12705381-chr18:12946243..12950219,9	K562	blood:
9	chr18:12882771..12885367-chr18:12946819..12949664,2	MCF-7	breast:
10	chr18:12945719..12950670-chr18:12989123..12995651,19	K562	blood:
11	chr18:12945869..12950267-chr18:12985686..12992743,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10163827	0.83[AMR][1000 genomes]
rs11080617	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11662634	0.82[AMR][1000 genomes]
rs11664469	0.86[AMR][1000 genomes]
rs12605267	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12953783	0.84[AMR][1000 genomes]
rs12957380	0.82[AMR][1000 genomes]
rs13381779	0.84[AMR][1000 genomes]
rs17603207	0.87[AMR][1000 genomes]
rs17659896	0.88[AMR][1000 genomes]
rs34166083	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34302481	0.88[AMR][1000 genomes]
rs35563947	0.88[AMR][1000 genomes]
rs3809914	0.80[AMR][1000 genomes]
rs3976787	0.80[AMR][1000 genomes]
rs68004799	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7239486	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8566	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	esv3450694	chr18:12933001-12955144	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	esv3342017	chr18:12946977-12949725	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12967249	CEP192	cis	Artery Tibial	GTEx
rs12967249	CEP192	cis	lung	GTEx
rs12967249	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs12967249	CEP192	cis	Thyroid	GTEx
rs12967249	CEP192	cis	Esophagus Muscularis	GTEx

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948600-12950000	ZNF genes & repeats	Fetal Intestine Large	intestine
2	chr18:12948800-12950000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr18:12948800-12950000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr18:12948800-12950000	ZNF genes & repeats	Fetal Thymus	thymus
5	chr18:12948800-12951000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:12948800-12951000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr18:12948800-12951000	Weak transcription	Spleen	Spleen
8	chr18:12948800-12951200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:12948800-12951600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr18:12948800-12951800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr18:12948800-12953400	Weak transcription	HUVEC	blood vessel
12	chr18:12948800-12954400	Weak transcription	NHDF-Ad	bronchial
13	chr18:12948800-12957600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr18:12948800-12958200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr18:12948800-12958200	Weak transcription	Left Ventricle	heart
16	chr18:12948800-12958400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr18:12948800-12958400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr18:12948800-12963200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr18:12948800-12963200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr18:12948800-12963200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:12948800-12963200	Weak transcription	Colon Smooth Muscle	Colon
22	chr18:12948800-12963600	Weak transcription	Esophagus	oesophagus
23	chr18:12948800-12971000	Weak transcription	Ovary	ovary
24	chr18:12948800-12971600	Weak transcription	Pancreas	Pancrea
25	chr18:12948800-12976600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr18:12949000-12949600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr18:12949000-12949600	Enhancers	Primary T cells from cord blood	blood
29	chr18:12949000-12949600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr18:12949000-12949800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr18:12949000-12949800	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr18:12949000-12950000	Enhancers	Fetal Brain Male	brain
33	chr18:12949000-12950200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr18:12949000-12950200	Enhancers	Primary B cells from cord blood	blood
35	chr18:12949000-12950200	Enhancers	Placenta	Placenta
36	chr18:12949000-12951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr18:12949000-12951000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr18:12949000-12951200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12949000-12952400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr18:12949000-12952400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr18:12949000-12952600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr18:12949000-12953000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr18:12949000-12953000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr18:12949000-12953200	Weak transcription	NH-A	brain
45	chr18:12949000-12953800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:12949000-12954600	Weak transcription	HSMMtube	muscle
47	chr18:12949000-12957400	Weak transcription	Fetal Lung	lung
48	chr18:12949000-12957400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr18:12949000-12957600	Weak transcription	Brain Angular Gyrus	brain
50	chr18:12949000-12957600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links