Variant report

Variant	rs132548
Chromosome Location	chr22:29317559-29317560
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29315873..29318298-chr22:29320072..29322086,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1065497	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12165962	0.82[CEU][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap]
rs1318025	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1318026	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs132528	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs132529	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs132531	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs132533	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs132536	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs132543	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs132561	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2015500	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2064261	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2097461	0.89[JPT][hapmap]
rs2213645	0.81[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap]
rs2239815	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[YRI][hapmap]
rs2239828	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2269577	0.89[JPT][hapmap]
rs2347447	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs3788409	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs469990	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs469991	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469992	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4822998	0.85[CHB][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap]
rs5752809	0.89[JPT][hapmap]
rs5752812	0.89[JPT][hapmap]
rs5752826	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762784	0.89[JPT][hapmap]
rs5762788	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs5762795	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap]
rs5762870	0.84[EUR][1000 genomes]
rs5762874	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762877	0.92[ASN][1000 genomes]
rs5762880	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5762881	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5762882	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5762936	0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs5997408	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap]
rs5997412	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6005881	0.89[JPT][hapmap];0.81[MEX][hapmap];0.95[YRI][hapmap]
rs6005915	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs6005936	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6519766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715531	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287806	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.95[YRI][hapmap]
rs7287918	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs763073	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[YRI][hapmap]
rs8137262	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8142067	0.86[EUR][1000 genomes]
rs9620841	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9625619	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs132548	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs132548	MN1	cis	cerebellum	SCAN
rs132548	ZNRF3	cis	parietal	SCAN
rs132548	GSTT1	cis	cerebellum	SCAN
rs132548	BEND4	trans	parietal	SCAN
rs132548	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29313200-29318600	Weak transcription	Spleen	Spleen
2	chr22:29314200-29318600	Weak transcription	Colonic Mucosa	Colon
3	chr22:29314200-29319800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:29314400-29318600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr22:29314400-29318800	Weak transcription	HMEC	breast
6	chr22:29314400-29342800	Weak transcription	Brain Substantia Nigra	brain
7	chr22:29314600-29321800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:29314800-29319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr22:29314800-29319800	Weak transcription	NH-A	brain
10	chr22:29314800-29328400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:29315000-29317600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr22:29315000-29317600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr22:29315000-29318600	Weak transcription	Aorta	Aorta
14	chr22:29315000-29318600	Weak transcription	Right Ventricle	heart
15	chr22:29315000-29319800	Weak transcription	Psoas Muscle	Psoas
16	chr22:29315200-29318600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr22:29315200-29318600	Weak transcription	Right Atrium	heart
18	chr22:29315200-29318800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr22:29315200-29318800	Weak transcription	Gastric	stomach
20	chr22:29315200-29319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr22:29315200-29319200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr22:29315200-29319800	Weak transcription	Fetal Brain Male	brain
23	chr22:29315200-29319800	Weak transcription	Left Ventricle	heart
24	chr22:29315200-29326400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:29315400-29318400	Weak transcription	Fetal Heart	heart
26	chr22:29315400-29318600	Weak transcription	Ovary	ovary
27	chr22:29315400-29318600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr22:29315400-29319000	Weak transcription	Brain Angular Gyrus	brain
29	chr22:29315400-29319800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr22:29315800-29325000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr22:29316000-29317600	Enhancers	GM12878-XiMat	blood
32	chr22:29316000-29317800	Enhancers	Liver	Liver
33	chr22:29316400-29317600	Enhancers	Pancreas	Pancrea
34	chr22:29316400-29318000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr22:29316400-29322600	Enhancers	Fetal Lung	lung
36	chr22:29316600-29317600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr22:29316600-29317600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr22:29316600-29317600	Flanking Active TSS	HepG2	liver
39	chr22:29316600-29317800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr22:29316600-29317800	Enhancers	Colon Smooth Muscle	Colon
41	chr22:29316600-29318000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:29316600-29319600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr22:29316600-29320000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr22:29316600-29322600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr22:29316800-29317600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr22:29316800-29317600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr22:29316800-29317600	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr22:29316800-29317600	Enhancers	Brain Hippocampus Middle	brain
49	chr22:29316800-29317600	Enhancers	Fetal Brain Female	brain
50	chr22:29316800-29317600	Enhancers	Fetal Intestine Large	intestine

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