Variant report

Variant	rs12889618
Chromosome Location	chr14:70789442-70789443
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12879256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12879701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880065	0.85[EUR][1000 genomes]
rs12885170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888630	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12889575	0.87[EUR][1000 genomes]
rs12890852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12897297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474359	0.82[EUR][1000 genomes]
rs17475333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17566073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17566625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17566723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17566814	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17566989	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28696763	0.81[EUR][1000 genomes]
rs34473038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34506335	0.85[EUR][1000 genomes]
rs34590849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34620351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34658788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34668417	0.82[EUR][1000 genomes]
rs34981619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35034872	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35224988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35543989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547503	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35697534	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35997384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66495513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67417438	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67434384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733739	0.82[EUR][1000 genomes]
rs72733767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902075	chr14:70612618-70919016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12889618	COX16	cis	Heart Left Ventricle	GTEx
rs12889618	RP11-718G2.3	cis	Muscle Skeletal	GTEx
rs12889618	COX16	cis	Muscle Skeletal	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70781200-70796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:70782600-70791800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr14:70782600-70791800	Weak transcription	HSMMtube	muscle
4	chr14:70783200-70792400	Weak transcription	HMEC	breast
5	chr14:70783400-70799200	Weak transcription	NHEK	skin
6	chr14:70783600-70791800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:70783600-70791800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr14:70783600-70792000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr14:70783600-70798600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:70784000-70792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:70784000-70792400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:70784000-70801000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr14:70784200-70792200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr14:70784200-70800600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:70784600-70790800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr14:70784600-70791000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr14:70784600-70798600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:70784800-70798800	Weak transcription	Gastric	stomach
19	chr14:70785000-70791200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr14:70785400-70790800	Weak transcription	A549	lung
21	chr14:70785400-70799200	Weak transcription	Stomach Mucosa	stomach
22	chr14:70785600-70799000	Weak transcription	Psoas Muscle	Psoas
23	chr14:70786000-70790800	Weak transcription	Liver	Liver
24	chr14:70786000-70794400	Weak transcription	Fetal Intestine Large	intestine
25	chr14:70786000-70794600	Weak transcription	Fetal Intestine Small	intestine
26	chr14:70786000-70799200	Weak transcription	Pancreas	Pancrea
27	chr14:70786400-70791200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr14:70786800-70792200	Weak transcription	HepG2	liver
29	chr14:70787000-70790400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr14:70787800-70790400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr14:70788200-70791200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr14:70788200-70813600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:70788400-70790800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr14:70788400-70790800	Weak transcription	Brain Germinal Matrix	brain
35	chr14:70788400-70791800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr14:70788400-70792400	Weak transcription	Osteobl	bone
37	chr14:70788600-70791000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr14:70788600-70791400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr14:70788600-70794400	Weak transcription	Left Ventricle	heart
40	chr14:70788800-70791400	Weak transcription	Adipose Nuclei	Adipose
41	chr14:70788800-70792200	Weak transcription	Brain Angular Gyrus	brain
42	chr14:70789000-70790400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:70789000-70790400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr14:70789000-70790600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr14:70789000-70791400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr14:70789000-70791800	Weak transcription	Lung	lung
47	chr14:70789000-70793600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr14:70789000-70798600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:70789200-70790800	Weak transcription	HSMM	muscle
50	chr14:70789200-70791800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links