Variant report

Variant	rs3848793
Chromosome Location	chr20:16247239-16247240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10485549	1.00[ASN][1000 genomes]
rs10485550	0.81[CEU][hapmap]
rs11907241	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16997595	1.00[JPT][hapmap]
rs17657892	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17730831	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730901	1.00[ASN][1000 genomes]
rs17731020	1.00[ASN][1000 genomes]
rs2144896	0.82[CHB][hapmap]
rs3848791	1.00[ASN][1000 genomes]
rs3848792	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052895	1.00[ASN][1000 genomes]
rs41276366	1.00[ASN][1000 genomes]
rs4416282	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4814466	1.00[ASN][1000 genomes]
rs4814467	1.00[ASN][1000 genomes]
rs57988134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105560	1.00[ASN][1000 genomes]
rs6105561	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105562	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105564	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs6111001	1.00[ASN][1000 genomes]
rs6111004	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6111005	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs6111007	1.00[ASN][1000 genomes]
rs6111008	1.00[ASN][1000 genomes]
rs6111025	1.00[CHB][hapmap]
rs718610	0.81[CEU][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv519621	chr20:16236837-16248453	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv516591	chr20:16238023-16248453	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3449914	chr20:16247143-16248367	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3848793	LOC100130264	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16244800-16253400	Weak transcription	Ovary	ovary
3	chr20:16245600-16248200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:16246400-16248000	ZNF genes & repeats	Fetal Muscle Leg	muscle
5	chr20:16246600-16247400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
6	chr20:16246600-16253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:16247200-16247400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr20:16247200-16248000	Weak transcription	Right Ventricle	heart
9	chr20:16247200-16248600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr20:16247200-16248600	ZNF genes & repeats	Fetal Stomach	stomach
11	chr20:16247200-16249000	ZNF genes & repeats	Aorta	Aorta

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