Variant report

Variant	rs4537545
Chromosome Location	chr1:154418879-154418880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11265613	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12126142	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12133641	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12730036	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12730935	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753254	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2228145	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4129267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4133213	0.86[ASN][1000 genomes]
rs4393147	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4453032	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4576655	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845371	0.88[ASW][hapmap]
rs4845372	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845373	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845620	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845621	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845623	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845625	0.94[ASW][hapmap];0.89[LWK][hapmap]
rs56383622	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61812598	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427658	0.81[ASW][hapmap]
rs6664201	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684439	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689393	0.94[ASW][hapmap];0.89[LWK][hapmap]
rs6694817	0.88[ASW][hapmap]
rs7512646	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518199	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521458	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7529229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
C-reactive protein	19567438	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4537545	LYSMD1	cis	cerebellum	SCAN
rs4537545	LINGO4	cis	parietal	SCAN
rs4537545	ANXA9	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:154408800-154420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:154408800-154420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:154409200-154420600	Weak transcription	Gastric	stomach
11	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
12	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
13	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
14	chr1:154412800-154425800	Weak transcription	HepG2	liver
15	chr1:154413000-154419600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:154413600-154419600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:154414400-154424400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:154414400-154424400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:154414600-154424400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:154414600-154426000	Weak transcription	Thymus	Thymus
22	chr1:154414800-154419000	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:154415000-154420600	Weak transcription	Pancreas	Pancrea
25	chr1:154415200-154419200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:154415200-154419200	Strong transcription	Lung	lung
27	chr1:154415200-154420800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:154415200-154424000	Weak transcription	Fetal Stomach	stomach
29	chr1:154415600-154419200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:154415600-154419200	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr1:154415800-154419400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:154415800-154425800	Weak transcription	Esophagus	oesophagus
33	chr1:154416200-154435800	Strong transcription	Liver	Liver
34	chr1:154416400-154420600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:154416600-154419800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:154416600-154420600	Weak transcription	Spleen	Spleen
37	chr1:154416600-154420800	Weak transcription	Right Ventricle	heart
38	chr1:154416600-154424400	Weak transcription	Colonic Mucosa	Colon
39	chr1:154416600-154425600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:154416800-154419200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:154416800-154420400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:154417200-154419000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:154417200-154419400	Enhancers	NHDF-Ad	bronchial
44	chr1:154417200-154419600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:154417200-154419600	Enhancers	NHLF	lung
46	chr1:154417400-154419400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:154417400-154419600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:154417400-154419600	Enhancers	NH-A	brain
49	chr1:154417400-154419600	Enhancers	Osteobl	bone
50	chr1:154417400-154428000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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