Variant report

Variant	rs16978516
Chromosome Location	chr18:43608511-43608512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10502871	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11082506	0.88[ASN][1000 genomes]
rs12606939	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16978517	0.85[ASN][1000 genomes]
rs4890310	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4890613	0.81[ASN][1000 genomes]
rs4890614	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4890615	0.92[ASN][1000 genomes]
rs57141604	0.83[ASN][1000 genomes]
rs58563731	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs609331	0.91[EUR][1000 genomes]
rs610186	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61423911	0.88[ASN][1000 genomes]
rs6507660	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6507661	0.84[ASN][1000 genomes]
rs6507662	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs654466	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68061103	0.92[ASN][1000 genomes]
rs8097830	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9675392	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43571400-43622000	Weak transcription	Gastric	stomach
2	chr18:43599600-43610600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:43601000-43619000	Weak transcription	K562	blood
4	chr18:43607800-43608600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr18:43607800-43608600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr18:43607800-43608600	Active TSS	Brain Cingulate Gyrus	brain
7	chr18:43607800-43608600	Active TSS	Brain Germinal Matrix	brain
8	chr18:43607800-43608600	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr18:43607800-43608800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr18:43607800-43608800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr18:43607800-43608800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr18:43607800-43608800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr18:43607800-43608800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr18:43607800-43608800	Active TSS	Colon Smooth Muscle	Colon
15	chr18:43607800-43608800	Active TSS	Fetal Brain Female	brain
16	chr18:43607800-43608800	Bivalent/Poised TSS	A549	lung
17	chr18:43607800-43609000	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr18:43607800-43609200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr18:43607800-43609200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr18:43608000-43608600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:43608000-43608600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr18:43608000-43608600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr18:43608000-43608600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr18:43608000-43608600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr18:43608000-43608600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr18:43608000-43608600	Active TSS	Brain Angular Gyrus	brain
27	chr18:43608000-43608600	Active TSS	HSMM	muscle
28	chr18:43608000-43608800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr18:43608000-43608800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr18:43608000-43608800	Active TSS	Muscle Satellite Cultured Cells	--
31	chr18:43608000-43608800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr18:43608000-43608800	Active TSS	Osteobl	bone
33	chr18:43608000-43614000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr18:43608200-43608600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr18:43608200-43608600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:43608200-43608600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:43608200-43608600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr18:43608200-43608600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:43608200-43608600	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr18:43608200-43608600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr18:43608200-43608600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
42	chr18:43608200-43608600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr18:43608200-43608600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr18:43608200-43608600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr18:43608200-43608600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr18:43608200-43608600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr18:43608200-43608600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr18:43608200-43608600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr18:43608200-43608600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr18:43608200-43608600	Flanking Active TSS	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links