Variant report

Variant	rs16939859
Chromosome Location	chr18:12789127-12789128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10502414	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10502415	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1065630	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17597893	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17598047	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17656120	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17656142	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17657106	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs2847288	1.00[CEU][hapmap]
rs45458596	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45506596	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45510799	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45518232	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45518540	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45575332	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45602843	0.86[EUR][1000 genomes]
rs45626137	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57450722	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57528860	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59368414	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59698881	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60617398	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402502	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73404411	0.97[EUR][1000 genomes]
rs73404414	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404420	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404421	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404424	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73404453	0.87[EUR][1000 genomes]
rs73414061	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8084006	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8085163	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8088256	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8092305	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs973767	0.81[EUR][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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

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	chr18:12776200-12791600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr18:12776200-12792600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr18:12776200-12794000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr18:12776200-12800800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr18:12776400-12800000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr18:12777400-12791400	Weak transcription	Left Ventricle	heart
12	chr18:12777600-12791800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr18:12777800-12791600	Weak transcription	Primary B cells from cord blood	blood
14	chr18:12777800-12791600	Weak transcription	Liver	Liver
15	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
16	chr18:12778000-12792800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:12778000-12801200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:12778200-12797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr18:12781200-12794200	Weak transcription	Spleen	Spleen
20	chr18:12782000-12811200	Weak transcription	Right Ventricle	heart
21	chr18:12782200-12794000	Weak transcription	Fetal Muscle Leg	muscle
22	chr18:12782600-12794000	Weak transcription	HSMMtube	muscle
23	chr18:12783200-12794200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr18:12783400-12794000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:12784000-12791800	Weak transcription	NHEK	skin
26	chr18:12784000-12792400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr18:12784000-12794000	Weak transcription	GM12878-XiMat	blood
28	chr18:12784000-12797600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr18:12784200-12791600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr18:12784200-12794000	Weak transcription	HMEC	breast
31	chr18:12784400-12792800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr18:12784400-12793800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:12784400-12794000	Weak transcription	Fetal Intestine Large	intestine
34	chr18:12784400-12801200	Weak transcription	Fetal Intestine Small	intestine
35	chr18:12784600-12793200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr18:12784600-12809000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr18:12785000-12803600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr18:12785400-12793000	Weak transcription	Adipose Nuclei	Adipose
39	chr18:12785400-12793200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr18:12786000-12793000	Weak transcription	Placenta	Placenta
41	chr18:12786000-12794000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:12786200-12793000	Weak transcription	HepG2	liver
43	chr18:12786200-12794000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr18:12786200-12794400	Weak transcription	Fetal Stomach	stomach
45	chr18:12786400-12790200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:12786800-12791400	Weak transcription	Primary T cells from cord blood	blood
47	chr18:12786800-12791600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:12786800-12799800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr18:12787000-12791800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr18:12787200-12791600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links