Variant report

Variant	rs2289800
Chromosome Location	chr13:110824823-110824824
allele	A/G
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:39)

rs_ID	r²[population]
rs1000989	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1000990	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562173	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1562174	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975472	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975491	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16975492	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1891964	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975514	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1977892	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1977893	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2005447	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2131937	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2131938	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2172725	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278673	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289799	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305080	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2391815	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2391816	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2391817	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3783111	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3783113	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs503053	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7325512	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7326444	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7329411	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874203	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874204	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515160	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9515161	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9521632	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9521633	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9521634	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9521635	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9521636	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9521637	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9521638	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9588108	0.93[AMR][1000 genomes];0.87[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	nsv1052147	chr13:110765635-110917782	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1045170	chr13:110815422-110836716	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv456116	chr13:110818598-110856153	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv563101	chr13:110818598-110856153	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110791200-110825600	Weak transcription	Esophagus	oesophagus
2	chr13:110791400-110825800	Weak transcription	A549	lung
3	chr13:110791400-110868400	Weak transcription	Psoas Muscle	Psoas
4	chr13:110795800-110826000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:110798400-110825400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:110798800-110825600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:110798800-110853200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:110799600-110840200	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:110800000-110825800	Strong transcription	Ovary	ovary
10	chr13:110800200-110837800	Strong transcription	NH-A	brain
11	chr13:110800600-110834200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:110802400-110842800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:110803000-110834200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:110803000-110840400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:110803200-110826000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:110803200-110839800	Weak transcription	NHDF-Ad	bronchial
17	chr13:110803200-110839800	Strong transcription	Osteobl	bone
18	chr13:110803600-110840000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr13:110804000-110825800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:110804800-110825200	Weak transcription	Brain Anterior Caudate	brain
21	chr13:110806600-110860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr13:110807800-110826200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr13:110809200-110840000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:110809600-110828000	Weak transcription	Fetal Brain Male	brain
25	chr13:110809800-110831200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr13:110810200-110866400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr13:110810400-110826000	Strong transcription	Aorta	Aorta
28	chr13:110810600-110825600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:110811000-110840200	Strong transcription	HUVEC	blood vessel
30	chr13:110811600-110830600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:110811800-110838800	Strong transcription	Right Ventricle	heart
32	chr13:110812000-110838800	Strong transcription	Left Ventricle	heart
33	chr13:110812400-110825600	Weak transcription	Fetal Heart	heart
34	chr13:110813800-110826400	Weak transcription	Brain Angular Gyrus	brain
35	chr13:110814200-110830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr13:110814800-110825800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr13:110816200-110840400	Strong transcription	Adipose Nuclei	Adipose
38	chr13:110817600-110825400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:110818400-110825200	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:110820600-110832200	Strong transcription	HSMMtube	muscle
41	chr13:110821000-110839400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr13:110821200-110826000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:110821200-110831000	Strong transcription	NHLF	lung
44	chr13:110821200-110831200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr13:110821600-110825600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr13:110821800-110825400	Strong transcription	Fetal Stomach	stomach
47	chr13:110821800-110825600	Strong transcription	Fetal Intestine Large	intestine
48	chr13:110822000-110825600	Strong transcription	Spleen	Spleen
49	chr13:110822000-110826200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr13:110822000-110839800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links