Variant report

Variant	rs1864220
Chromosome Location	chr5:15622094-15622095
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10434654	0.82[JPT][hapmap]
rs10520819	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1127792	0.91[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs12515169	0.82[JPT][hapmap]
rs12516275	0.82[JPT][hapmap]
rs12517648	0.82[JPT][hapmap]
rs12518052	0.82[JPT][hapmap]
rs12519070	0.82[JPT][hapmap]
rs12520060	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12522526	0.82[JPT][hapmap]
rs12522561	0.82[JPT][hapmap]
rs12655750	0.82[JPT][hapmap]
rs16867529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867549	0.82[JPT][hapmap]
rs16867589	0.82[JPT][hapmap]
rs17647689	0.82[JPT][hapmap]
rs17647713	0.82[JPT][hapmap]
rs17647898	0.82[JPT][hapmap]
rs17648198	0.82[JPT][hapmap]
rs17704227	0.82[JPT][hapmap]
rs17704245	0.82[JPT][hapmap]
rs4296803	0.82[JPT][hapmap]
rs4377704	0.82[JPT][hapmap]
rs4391162	0.82[JPT][hapmap]
rs4593267	0.82[JPT][hapmap]
rs4627983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4701643	0.82[JPT][hapmap]
rs59221558	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62347909	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62347910	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62347911	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62347912	0.87[ASN][1000 genomes]
rs62347915	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62347934	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62347936	0.90[EUR][1000 genomes]
rs6870504	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637832	0.82[JPT][hapmap]
rs9790923	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv4732	chr5:15598325-15636520	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1864220	CDH18	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15585000-15630200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:15593400-15633400	Weak transcription	Fetal Lung	lung
3	chr5:15600600-15645400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:15610000-15627400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:15610400-15635200	Weak transcription	Fetal Stomach	stomach
6	chr5:15613600-15635200	Weak transcription	Right Ventricle	heart
7	chr5:15619800-15622200	Enhancers	HUVEC	blood vessel
8	chr5:15620800-15622200	Enhancers	Fetal Heart	heart
9	chr5:15620800-15635000	Weak transcription	Lung	lung
10	chr5:15620800-15635400	Weak transcription	Psoas Muscle	Psoas
11	chr5:15621400-15624600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:15621400-15630000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:15621400-15635400	Weak transcription	Aorta	Aorta
14	chr5:15621600-15627000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:15621800-15622200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:15621800-15624200	Weak transcription	Ovary	ovary
17	chr5:15621800-15624400	Weak transcription	Brain Anterior Caudate	brain
18	chr5:15621800-15625000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:15621800-15625000	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:15621800-15627200	Weak transcription	HSMMtube	muscle
21	chr5:15621800-15627400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:15621800-15629200	Weak transcription	Left Ventricle	heart
23	chr5:15621800-15629600	Weak transcription	HSMM	muscle
24	chr5:15622000-15622200	Enhancers	NHDF-Ad	bronchial
25	chr5:15622000-15626600	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:15622000-15627200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links