Variant report

Variant	rs2451744
Chromosome Location	chr6:26633463-26633464
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABT1-5	chr6:26630055-26634786	NONHSAT108301

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1021372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1021373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027203	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1027204	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13207371	0.84[EUR][1000 genomes]
rs1490488	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2130657	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2172007	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2451711	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451712	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451731	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451740	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451741	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494692	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494700	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2494701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494709	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494713	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2494716	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2498351	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2498380	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2504566	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504567	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504571	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504600	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2758383	0.82[EUR][1000 genomes]
rs3001369	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34453863	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3800303	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4368798	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62394558	0.82[EUR][1000 genomes]
rs6925087	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7767847	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461273	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461275	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461276	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461288	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9467802	0.81[ASN][1000 genomes]
rs9467804	0.83[ASN][1000 genomes]
rs9467805	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467810	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467831	0.80[EUR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2451744	RP11-457M11.2	cis	Thyroid	GTEx
rs2451744	RP11-457M11.2	cis	lung	GTEx
rs2451744	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2451744	ZNF322	cis	Artery Tibial	GTEx
rs2451744	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs2451744	ZNF322	cis	Nerve Tibial	GTEx
rs2451744	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2451744	ZNF322A	cis	multi-tissue	Pritchard
rs2451744	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs2451744	ZNF322	cis	Thyroid	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26625400-26639200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:26629400-26639200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:26629600-26635400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:26629800-26640000	Weak transcription	Left Ventricle	heart
5	chr6:26630400-26640000	Weak transcription	Aorta	Aorta
6	chr6:26630600-26633600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:26631200-26633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:26631200-26634000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:26631400-26634600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:26631400-26639000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:26631800-26634200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:26631800-26634400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:26631800-26634800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:26631800-26639200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:26631800-26640400	Weak transcription	Pancreas	Pancrea
16	chr6:26632000-26633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:26632000-26633800	Weak transcription	Adipose Nuclei	Adipose
18	chr6:26632000-26640600	Weak transcription	Fetal Stomach	stomach
19	chr6:26632200-26633800	Weak transcription	Brain Angular Gyrus	brain
20	chr6:26632200-26633800	Weak transcription	HSMMtube	muscle
21	chr6:26632200-26634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:26632200-26634000	Weak transcription	Brain Anterior Caudate	brain
23	chr6:26632200-26634000	Weak transcription	Fetal Brain Female	brain
24	chr6:26632200-26634000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:26632200-26639000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:26632200-26639200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:26632200-26639200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:26632400-26633800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:26632400-26634000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:26632400-26634600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:26632400-26639000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:26632600-26633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:26632600-26638200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:26632600-26638800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:26632600-26638800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:26632600-26639000	Weak transcription	Dnd41	blood
37	chr6:26632600-26640000	Weak transcription	Fetal Kidney	kidney
38	chr6:26632800-26634400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:26632800-26634600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:26632800-26638400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:26632800-26639000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:26632800-26639200	Weak transcription	Psoas Muscle	Psoas
43	chr6:26632800-26640000	Weak transcription	Esophagus	oesophagus
44	chr6:26633000-26634400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:26633000-26639000	Weak transcription	HepG2	liver
46	chr6:26633000-26639200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:26633000-26639200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:26633000-26639200	Weak transcription	Right Ventricle	heart
49	chr6:26633000-26639400	Weak transcription	Colonic Mucosa	Colon
50	chr6:26633000-26640400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links