Variant report

Variant	rs4356203
Chromosome Location	chr11:17160148-17160149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10832733	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs10832739	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10832743	0.83[EUR][1000 genomes]
rs10832747	0.81[CEU][hapmap]
rs11024148	0.89[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11024158	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11024159	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11024163	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11024204	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs12280930	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12286505	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1236309	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12801545	0.85[EUR][1000 genomes]
rs12804000	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1685932	0.83[EUR][1000 genomes]
rs1989405	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2008905	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052188	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214082	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs214083	0.92[JPT][hapmap]
rs214092	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs214093	0.92[JPT][hapmap]
rs214097	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs214900	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs214901	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs214906	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214910	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs214914	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs214925	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs214927	0.88[CEU][hapmap]
rs214933	0.87[CHD][hapmap]
rs214935	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs214936	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs214937	0.83[EUR][1000 genomes]
rs214939	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214940	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs511119	0.83[EUR][1000 genomes]
rs512852	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs527810	0.81[EUR][1000 genomes]
rs536628	0.83[EUR][1000 genomes]
rs545773	0.83[EUR][1000 genomes]
rs550667	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs553711	0.82[EUR][1000 genomes]
rs577207	0.82[EUR][1000 genomes]
rs589319	0.83[EUR][1000 genomes]
rs594034	0.82[EUR][1000 genomes]
rs598946	0.83[EUR][1000 genomes]
rs603618	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs615358	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs618331	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs620241	0.83[EUR][1000 genomes]
rs621246	0.83[EUR][1000 genomes]
rs635802	0.83[EUR][1000 genomes]
rs6486352	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6486354	0.83[EUR][1000 genomes]
rs651513	0.82[EUR][1000 genomes]
rs656623	0.83[EUR][1000 genomes]
rs662711	0.83[EUR][1000 genomes]
rs667984	0.83[EUR][1000 genomes]
rs677540	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs680205	0.83[EUR][1000 genomes]
rs7118006	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7123301	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7125607	0.88[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs7342262	0.88[CEU][hapmap]
rs7396382	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7396958	0.84[EUR][1000 genomes]
rs7478986	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7925692	0.88[CEU][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs7927240	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs7935219	0.84[EUR][1000 genomes]
rs7937176	0.88[CEU][hapmap]
rs7938820	0.89[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs7946010	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7949699	0.92[CEU][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv7691	chr11:17151593-17196894	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Schizophrenia	21926974	GWAS catalog
Schizophrenia or bipolar disorder	24280982	GWAS catalog

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4356203	MYOD1	cis	parietal	SCAN
rs4356203	SAA4	cis	parietal	SCAN
rs4356203	GTF2H1	cis	cerebellum	SCAN
rs4356203	RNU14	cis	multi-tissue	Pritchard
rs4356203	ABCC8	cis	parietal	SCAN
rs4356203	PDE3B	cis	parietal	SCAN
rs4356203	NUCB2	cis	multi-tissue	Pritchard
rs4356203	NUCB2	cis	lymphoblastoid	seeQTL
rs4356203	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs4356203	SPTY2D1	cis	parietal	SCAN
rs4356203	OR7E14P	cis	Esophagus Mucosa	GTEx
rs4356203	OR7E14P	cis	Nerve Tibial	GTEx
rs4356203	SOX6	cis	parietal	SCAN
rs4356203	ABCC8	cis	cerebellum	SCAN
rs4356203	NUCB2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17105400-17172800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:17107000-17167200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:17108200-17177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:17108600-17172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:17111600-17182000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:17120400-17181600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:17120800-17166200	Weak transcription	Pancreas	Pancrea
8	chr11:17120800-17171800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:17120800-17172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:17121000-17178000	Weak transcription	Psoas Muscle	Psoas
11	chr11:17125400-17172200	Weak transcription	Fetal Brain Male	brain
12	chr11:17125800-17181400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:17126800-17186400	Weak transcription	Colonic Mucosa	Colon
14	chr11:17130200-17174600	Weak transcription	Spleen	Spleen
15	chr11:17130200-17203800	Weak transcription	Aorta	Aorta
16	chr11:17132000-17167800	Weak transcription	Right Ventricle	heart
17	chr11:17132200-17163200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:17139000-17171200	Weak transcription	Fetal Brain Female	brain
19	chr11:17140000-17183400	Weak transcription	Small Intestine	intestine
20	chr11:17143000-17163800	Weak transcription	Gastric	stomach
21	chr11:17144200-17192800	Weak transcription	NHDF-Ad	bronchial
22	chr11:17144600-17166600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:17150800-17165800	Weak transcription	HMEC	breast
24	chr11:17150800-17172000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:17150800-17186000	Weak transcription	NHLF	lung
26	chr11:17151000-17163000	Weak transcription	Hela-S3	cervix
27	chr11:17151000-17165400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:17151000-17173200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:17152400-17160400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:17153200-17160400	Strong transcription	Placenta	Placenta
31	chr11:17154600-17166600	Weak transcription	Ovary	ovary
32	chr11:17155000-17161600	Weak transcription	HSMM	muscle
33	chr11:17155000-17166600	Weak transcription	Fetal Kidney	kidney
34	chr11:17155200-17163400	Weak transcription	NHEK	skin
35	chr11:17155600-17163800	Weak transcription	Primary B cells from cord blood	blood
36	chr11:17156400-17160400	Weak transcription	Fetal Intestine Small	intestine
37	chr11:17156400-17162000	Weak transcription	Brain Substantia Nigra	brain
38	chr11:17156400-17186400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr11:17156400-17186600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:17156600-17161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:17156600-17161600	Weak transcription	Left Ventricle	heart
42	chr11:17156600-17162000	Weak transcription	Fetal Lung	lung
43	chr11:17156600-17162200	Weak transcription	Fetal Thymus	thymus
44	chr11:17156600-17163200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:17156600-17163200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr11:17156600-17163800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr11:17156600-17164000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:17156600-17164000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:17156600-17164000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:17156600-17164000	Weak transcription	Fetal Stomach	stomach

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