Variant report

Variant	rs1921778
Chromosome Location	chr2:206081610-206081611
allele	C/T
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:18)

rs_ID	r²[population]
rs13425339	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1921789	0.82[EUR][1000 genomes]
rs1921790	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1921796	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2161027	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856508	0.86[AMR][1000 genomes]
rs6435278	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6722362	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6728864	0.89[ASN][1000 genomes]
rs6730457	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6746095	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6750663	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6752947	0.87[AMR][1000 genomes]
rs7560089	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7561723	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7583368	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs759779	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7597894	1.00[AMR][1000 genomes];0.83[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	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv16739	chr2:205898770-206127984	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv875730	chr2:206057649-206093367	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1921778	RAPH1	cis	cerebellum	SCAN
rs1921778	CRYGC	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:206075200-206100000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:206079800-206084400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:206081000-206098600	Weak transcription	Fetal Lung	lung
4	chr2:206081400-206082000	Enhancers	Ovary	ovary
5	chr2:206081400-206082000	Enhancers	HepG2	liver
6	chr2:206081400-206094200	Weak transcription	Fetal Intestine Small	intestine
7	chr2:206081600-206081800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:206081600-206081800	Enhancers	Gastric	stomach
9	chr2:206081600-206082000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:206081600-206082000	Enhancers	HUES48 Cell Line	embryonic stem cell

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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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