Variant report

Variant	rs2425473
Chromosome Location	chr20:40730515-40730516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1126101	0.80[CEU][hapmap]
rs1126102	0.82[EUR][1000 genomes]
rs1883375	0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1883380	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076247	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2143004	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2425469	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2425470	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2425471	0.93[ASN][1000 genomes]
rs2425472	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2425475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866942	0.88[ASN][1000 genomes]
rs2866947	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3091600	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3091875	0.89[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3091889	0.93[ASN][1000 genomes]
rs3091932	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs3092252	0.93[ASN][1000 genomes]
rs3092503	0.93[ASN][1000 genomes]
rs3092588	0.93[ASN][1000 genomes]
rs3092614	0.93[ASN][1000 genomes]
rs6130027	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7263976	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs750782	0.80[CEU][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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2425473	YWHAB	cis	cerebellum	SCAN
rs2425473	DHX35	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40715800-40757600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40722800-40747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:40723200-40741400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:40725200-40730800	Enhancers	Fetal Intestine Small	intestine
5	chr20:40725200-40731200	Enhancers	Fetal Intestine Large	intestine
6	chr20:40728400-40731400	Enhancers	Pancreas	Pancrea
7	chr20:40728600-40730800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr20:40729600-40731000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:40730000-40731200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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