Variant report

Variant	rs4785521
Chromosome Location	chr16:48532560-48532561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1001872	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1004704	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11076569	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11641936	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11643514	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11648225	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11865776	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1566466	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1566467	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1948713	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2062553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062555	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088753	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088754	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4028695	0.89[CEU][hapmap]
rs4785244	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4785520	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55745119	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56207849	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6500390	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7184700	0.82[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs7189631	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7194822	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7198215	0.80[ASN][1000 genomes]
rs7198420	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7202699	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7203475	0.80[ASN][1000 genomes]
rs7206781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8046716	0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs8052026	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8054389	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8054696	0.80[ASN][1000 genomes]
rs8056201	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8056346	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8057027	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8063059	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9888862	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9889065	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9889067	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9921402	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9923092	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9925108	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9925138	0.92[EUR][1000 genomes]
rs9926683	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9933892	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9937129	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939368	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939554	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9940599	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941289	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1800739	chr16:48418505-48560315	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv428658	chr16:48438656-48587750	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1817281	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1842977	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1849228	chr16:48509311-48537421	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1065358	chr16:48513824-48554254	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1064323	chr16:48531171-48573066	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1060196	chr16:48531171-48578101	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4785521	NOD2	cis	cerebellum	SCAN
rs4785521	PAPD5	cis	cerebellum	SCAN
rs4785521	NKD1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48526400-48533000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:48529600-48534000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr16:48531000-48538600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr16:48531200-48538800	Enhancers	Fetal Stomach	stomach
5	chr16:48531600-48533200	Enhancers	Pancreas	Pancrea
6	chr16:48531600-48534400	Enhancers	Liver	Liver
7	chr16:48531800-48533000	Enhancers	Fetal Lung	lung
8	chr16:48531800-48533400	Enhancers	Fetal Muscle Trunk	muscle
9	chr16:48531800-48536200	Enhancers	Fetal Muscle Leg	muscle
10	chr16:48532000-48532800	Enhancers	Hela-S3	cervix
11	chr16:48532000-48533200	Enhancers	Spleen	Spleen
12	chr16:48532000-48533800	Enhancers	Placenta	Placenta
13	chr16:48532200-48532600	Enhancers	Psoas Muscle	Psoas
14	chr16:48532200-48532600	Flanking Active TSS	HepG2	liver
15	chr16:48532200-48533200	Enhancers	Right Atrium	heart
16	chr16:48532200-48533200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr16:48532200-48533200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr16:48532200-48533400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:48532200-48533400	Enhancers	Ovary	ovary
20	chr16:48532400-48532600	Enhancers	Duodenum Mucosa	Duodenum
21	chr16:48532400-48533200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:48532400-48533200	Enhancers	Right Ventricle	heart
23	chr16:48532400-48533200	Enhancers	Stomach Smooth Muscle	stomach
24	chr16:48532400-48533400	Enhancers	Fetal Kidney	kidney
25	chr16:48532400-48541800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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