Variant report

Variant	rs9955973
Chromosome Location	chr18:7939863-7939864
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12103962	0.83[AMR][1000 genomes]
rs2099932	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28367342	1.00[AMR][1000 genomes]
rs28379285	1.00[AMR][1000 genomes]
rs28521877	0.83[AMR][1000 genomes]
rs28523954	0.83[AMR][1000 genomes]
rs28569201	1.00[AMR][1000 genomes]
rs28644497	0.83[AMR][1000 genomes]
rs28757770	0.83[AMR][1000 genomes]
rs6506541	0.83[AMR][1000 genomes]
rs7239724	0.83[AMR][1000 genomes]
rs7239846	0.83[AMR][1000 genomes]
rs7241071	0.83[AMR][1000 genomes]
rs73385648	0.83[AMR][1000 genomes]
rs73385649	0.83[AMR][1000 genomes]
rs73385658	0.83[AMR][1000 genomes]
rs73385659	0.83[AMR][1000 genomes]
rs9945054	0.83[AMR][1000 genomes]
rs9948263	1.00[AMR][1000 genomes]
rs9949297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9950590	0.83[AMR][1000 genomes]
rs9951398	0.83[AMR][1000 genomes]
rs9952873	0.83[AMR][1000 genomes]
rs9952921	1.00[AMR][1000 genomes]
rs9955097	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9958058	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9963467	1.00[AMR][1000 genomes]
rs9963748	0.83[AMR][1000 genomes]
rs9965536	0.83[AMR][1000 genomes]
rs9966712	0.83[AMR][1000 genomes]
rs9966934	0.83[AMR][1000 genomes]
rs9967327	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv2761987	chr18:7934001-7943335	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7922400-7940600	Weak transcription	Gastric	stomach
2	chr18:7923400-7945800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr18:7924400-7940400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:7925800-7940400	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:7926400-7940200	Weak transcription	Brain Germinal Matrix	brain
6	chr18:7926400-7945200	Weak transcription	Ovary	ovary
7	chr18:7926800-7945600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr18:7926800-7945800	Weak transcription	Fetal Lung	lung
9	chr18:7927400-7940200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr18:7927800-7946600	Weak transcription	Fetal Kidney	kidney
11	chr18:7928000-7946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:7932000-7946000	Weak transcription	Brain Anterior Caudate	brain
13	chr18:7932200-7961000	Weak transcription	HepG2	liver
14	chr18:7933400-7940400	Weak transcription	Lung	lung
15	chr18:7933600-7945400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr18:7933800-7940000	Weak transcription	Right Atrium	heart
17	chr18:7934200-7941000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr18:7936800-7940400	Weak transcription	Aorta	Aorta
19	chr18:7936800-7941000	Weak transcription	Pancreas	Pancrea
20	chr18:7936800-7944800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr18:7937200-7945800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:7937400-7945600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr18:7937600-7940400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr18:7937600-7940400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr18:7937600-7945600	Weak transcription	Fetal Stomach	stomach
26	chr18:7937600-7947000	Weak transcription	Thymus	Thymus
27	chr18:7937600-7949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr18:7937600-7955200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr18:7937800-7940400	Weak transcription	Adipose Nuclei	Adipose
30	chr18:7938000-7940000	Weak transcription	Right Ventricle	heart
31	chr18:7938000-7940400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr18:7938000-7945600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr18:7938000-7945600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr18:7938000-7946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr18:7939200-7941800	Enhancers	Left Ventricle	heart
36	chr18:7939800-7940200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr18:7939800-7940800	Weak transcription	Fetal Brain Female	brain
38	chr18:7939800-7941400	Enhancers	Psoas Muscle	Psoas
39	chr18:7939800-7942000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr18:7939800-7942600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links