Variant report

Variant	rs2289987
Chromosome Location	chr11:36298191-36298192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11033524	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033527	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602024	0.84[AFR][1000 genomes]
rs11603166	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12361221	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1562327	0.80[EUR][1000 genomes]
rs1900336	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289986	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4418777	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56386213	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61878683	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61878687	0.87[EUR][1000 genomes]
rs6484831	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104737	0.84[ASN][1000 genomes]
rs7107433	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109505	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72946165	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7951298	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9667667	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787880	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9787894	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9888212	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9888261	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2289987	LINC00610	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36280400-36299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:36280800-36300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:36282200-36302000	Weak transcription	NHEK	skin
4	chr11:36283200-36300000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:36287600-36304800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:36288000-36310200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:36288400-36304600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:36289200-36299800	Weak transcription	HepG2	liver
9	chr11:36289200-36300000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:36290800-36310400	Weak transcription	Stomach Mucosa	stomach
11	chr11:36291000-36298200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:36291000-36298400	Strong transcription	Fetal Stomach	stomach
13	chr11:36291000-36301200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:36291000-36301800	Weak transcription	Right Atrium	heart
15	chr11:36291200-36299000	Strong transcription	Adipose Nuclei	Adipose
16	chr11:36291200-36299000	Strong transcription	Ovary	ovary
17	chr11:36291200-36299200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:36291200-36299400	Strong transcription	Brain Angular Gyrus	brain
19	chr11:36291200-36299400	Strong transcription	Brain Hippocampus Middle	brain
20	chr11:36291200-36302200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr11:36291200-36302400	Strong transcription	Primary T cells from cord blood	blood
22	chr11:36291200-36302800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:36291400-36298400	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr11:36291400-36298800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:36291400-36303000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:36291800-36301200	Strong transcription	Fetal Intestine Large	intestine
27	chr11:36291800-36302200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr11:36292000-36298200	Strong transcription	Brain Anterior Caudate	brain
29	chr11:36292000-36298200	Strong transcription	Brain Germinal Matrix	brain
30	chr11:36292000-36298200	Strong transcription	Thymus	Thymus
31	chr11:36292000-36298800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:36292000-36299000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:36292000-36302000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:36292000-36302400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr11:36292000-36303200	Strong transcription	Primary B cells from cord blood	blood
36	chr11:36292000-36309600	Weak transcription	Psoas Muscle	Psoas
37	chr11:36292200-36298800	Strong transcription	Gastric	stomach
38	chr11:36292200-36299200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:36292200-36301200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:36292200-36302200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:36292200-36302200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:36292200-36302400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:36292200-36309600	Weak transcription	A549	lung
44	chr11:36292400-36302000	Strong transcription	Liver	Liver
45	chr11:36292400-36302200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:36292400-36302400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:36292600-36298200	Strong transcription	Rectal Smooth Muscle	rectum
48	chr11:36292600-36298400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:36292600-36298800	Strong transcription	Esophagus	oesophagus
50	chr11:36292600-36298800	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links