Variant report

Variant	rs45450798
Chromosome Location	chr18:12792940-12792941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12786405..12788580-chr18:12791751..12793995,2	K562	blood:
2	chr18:12791783..12794622-chr18:12801146..12803665,2	K562	blood:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11663253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014857	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542147	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542148	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542149	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542150	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542151	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847259	0.91[ASN][1000 genomes]
rs2847260	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847274	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847278	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847280	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847293	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34920518	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60474474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60735058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60751993	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7237497	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8096138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888270	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs45450798	RP11-973H7.1	cis	Artery Tibial	GTEx
rs45450798	RP11-973H7.1	cis	lung	GTEx
rs45450798	RP11-973H7.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767400-12815800	Weak transcription	Gastric	stomach
2	chr18:12776000-12793600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr18:12776200-12794000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr18:12776200-12800800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr18:12776400-12800000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
10	chr18:12778000-12801200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:12778200-12797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:12781200-12794200	Weak transcription	Spleen	Spleen
13	chr18:12782000-12811200	Weak transcription	Right Ventricle	heart
14	chr18:12782200-12794000	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:12782600-12794000	Weak transcription	HSMMtube	muscle
16	chr18:12783200-12794200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:12783400-12794000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr18:12784000-12794000	Weak transcription	GM12878-XiMat	blood
19	chr18:12784000-12797600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr18:12784200-12794000	Weak transcription	HMEC	breast
21	chr18:12784400-12793800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr18:12784400-12794000	Weak transcription	Fetal Intestine Large	intestine
23	chr18:12784400-12801200	Weak transcription	Fetal Intestine Small	intestine
24	chr18:12784600-12793200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:12784600-12809000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr18:12785000-12803600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr18:12785400-12793000	Weak transcription	Adipose Nuclei	Adipose
28	chr18:12785400-12793200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr18:12786000-12793000	Weak transcription	Placenta	Placenta
30	chr18:12786000-12794000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr18:12786200-12793000	Weak transcription	HepG2	liver
32	chr18:12786200-12794000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr18:12786200-12794400	Weak transcription	Fetal Stomach	stomach
34	chr18:12786800-12799800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr18:12787200-12793800	Weak transcription	Brain Anterior Caudate	brain
36	chr18:12787400-12794000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr18:12787400-12808800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr18:12787600-12794000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr18:12787600-12815800	Weak transcription	Pancreas	Pancrea
40	chr18:12788400-12802000	Weak transcription	Colon Smooth Muscle	Colon
41	chr18:12788600-12794000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr18:12788600-12795200	Strong transcription	Dnd41	blood
43	chr18:12788600-12795600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr18:12788800-12794000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:12789000-12793800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr18:12789000-12802600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr18:12789000-12821400	Weak transcription	Small Intestine	intestine
48	chr18:12789200-12814200	Weak transcription	Fetal Kidney	kidney
49	chr18:12789600-12794200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr18:12789600-12808800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links