Variant report

Variant	rs396106
Chromosome Location	chr1:76055098-76055099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1332784	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1332790	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17303921	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs182411	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211675	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211678	0.83[ASN][1000 genomes]
rs211679	0.83[ASN][1000 genomes]
rs211683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs211688	0.83[CEU][hapmap]
rs211696	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211759	1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs211762	0.92[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs211786	0.85[CHB][hapmap]
rs377233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417258	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs434424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs396106	CRYZ	cis	lymphoblastoid	seeQTL
rs396106	IFI44	cis	parietal	SCAN
rs396106	SLC44A5	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76052400-76055200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:76053600-76060400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:76053800-76055200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:76053800-76055400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:76053800-76055400	Weak transcription	Gastric	stomach
6	chr1:76053800-76055400	Weak transcription	Pancreas	Pancrea
7	chr1:76054400-76055800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:76054600-76055800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:76054600-76056000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:76054800-76055600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:76054800-76055600	Enhancers	Stomach Mucosa	stomach
12	chr1:76054800-76055800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:76054800-76055800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:76055000-76055400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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