Variant report

Variant	rs469992
Chromosome Location	chr22:29314899-29314900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1065497	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1318025	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1318026	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs132528	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs132529	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs132531	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs132533	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs132536	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs132543	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs132548	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015500	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2064261	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs469990	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469991	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752826	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5762870	0.88[EUR][1000 genomes]
rs5762874	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5762877	0.90[ASN][1000 genomes]
rs5762880	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5762881	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762882	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997412	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6005936	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6519766	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs715531	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7287918	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8137262	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8142067	0.87[EUR][1000 genomes]
rs9620841	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625619	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs469992	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29311600-29315600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:29311600-29316000	Enhancers	Fetal Lung	lung
3	chr22:29312000-29315800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:29312200-29315200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:29312200-29315800	Enhancers	Fetal Muscle Leg	muscle
6	chr22:29312200-29316000	Enhancers	Placenta	Placenta
7	chr22:29312400-29315200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr22:29312400-29315200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr22:29312400-29315200	Enhancers	Fetal Brain Female	brain
10	chr22:29312400-29315400	Enhancers	Brain Anterior Caudate	brain
11	chr22:29312400-29315400	Enhancers	Ovary	ovary
12	chr22:29312400-29315600	Enhancers	Fetal Stomach	stomach
13	chr22:29312600-29315000	Enhancers	Psoas Muscle	Psoas
14	chr22:29312600-29315200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr22:29312600-29315200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29312600-29315200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:29312600-29315200	Enhancers	Fetal Brain Male	brain
18	chr22:29312600-29315200	Enhancers	Fetal Intestine Large	intestine
19	chr22:29312600-29315200	Enhancers	Left Ventricle	heart
20	chr22:29312600-29315400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr22:29312600-29315400	Enhancers	Brain Angular Gyrus	brain
22	chr22:29312600-29316000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr22:29312800-29315000	Enhancers	Right Ventricle	heart
24	chr22:29312800-29315200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr22:29312800-29315400	Enhancers	Brain Cingulate Gyrus	brain
26	chr22:29312800-29315400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr22:29313000-29315000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr22:29313000-29315000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr22:29313000-29315000	Enhancers	Lung	lung
30	chr22:29313000-29315000	Enhancers	Pancreas	Pancrea
31	chr22:29313000-29315200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr22:29313000-29315200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr22:29313000-29315200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:29313000-29315200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr22:29313000-29315200	Enhancers	Right Atrium	heart
36	chr22:29313000-29315200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr22:29313000-29315200	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr22:29313000-29315800	Enhancers	Fetal Muscle Trunk	muscle
39	chr22:29313200-29315000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr22:29313200-29315000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr22:29313200-29315200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr22:29313200-29315200	Enhancers	Gastric	stomach
43	chr22:29313200-29315200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr22:29313200-29315200	Enhancers	Stomach Mucosa	stomach
45	chr22:29313200-29315400	Enhancers	Brain Hippocampus Middle	brain
46	chr22:29313200-29318600	Weak transcription	Spleen	Spleen
47	chr22:29313600-29315000	Enhancers	Aorta	Aorta
48	chr22:29313600-29315200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr22:29313800-29315000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr22:29313800-29315000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links