Variant report

Variant	rs4550657
Chromosome Location	chr2:230990660-230990661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10176604	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10183352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183531	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194896	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11895353	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11895360	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12611791	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12694830	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12694836	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12694837	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13007948	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436908	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7589000	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9653375	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	esv2751843	chr2:230667570-230993134	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1007920	chr2:230775427-231065592	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv875942	chr2:230959532-231008980	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv875943	chr2:230960946-231027162	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2830298	chr2:230988148-230995447	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4550657	ALPI	cis	parietal	SCAN
rs4550657	SP100	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:230989000-230990800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr2:230989000-230992200	Enhancers	Spleen	Spleen
3	chr2:230989400-230993800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:230989800-230992800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr2:230989800-230992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:230990000-230993600	Weak transcription	Placenta	Placenta
7	chr2:230990200-230991200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:230990200-230993000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:230990400-230991000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:230990400-230992800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:230990400-230992800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr2:230990400-230993200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:230990600-230992800	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:230990600-230993400	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:230990600-230993800	Weak transcription	Brain Substantia Nigra	brain

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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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