Variant report

Variant	rs2850393
Chromosome Location	chr4:102955216-102955217
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11947367	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12640056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12649238	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17031983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17031995	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2450406	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2450407	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631269	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2631270	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850374	0.83[JPT][hapmap]
rs34184671	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35880229	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6842661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7693723	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2757945	chr4:102662699-103008940	Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2759269	chr4:102662699-103008940	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1011180	chr4:102685236-102985945	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537202	chr4:102685236-102985945	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879682	chr4:102859835-103088491	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv461596	chr4:102935902-103008712	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv594955	chr4:102935902-103008712	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2850393	ADH4	cis	cerebellum	SCAN
rs2850393	PPA2	cis	cerebellum	SCAN
rs2850393	RAP1GDS1	cis	cerebellum	SCAN
rs2850393	GSTCD	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102942600-102958600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:102947400-102957800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:102948400-102965400	Strong transcription	Primary B cells from cord blood	blood
4	chr4:102951800-102979200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr4:102955200-102955600	Enhancers	Pancreatic Islets	Pancreatic Islet

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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