Variant report

Variant	rs41357249
Chromosome Location	chr1:226397002-226397003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1043641	0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs10915943	1.00[YRI][hapmap]
rs11577454	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap]
rs11802954	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs11811952	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs12402078	1.00[YRI][hapmap]
rs17575721	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs28621419	0.82[ASN][1000 genomes]
rs4082281	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66527714	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66950676	0.81[ASN][1000 genomes]
rs67392783	0.81[ASN][1000 genomes]
rs67810611	0.86[ASN][1000 genomes]
rs72759091	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72759098	0.87[AMR][1000 genomes]
rs7521958	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs9659181	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662238	1.00[YRI][hapmap]
rs9725713	1.00[YRI][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	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41357249	FBXO28	cis	cerebellum	SCAN
rs41357249	DEGS1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226375200-226411000	Weak transcription	Right Atrium	heart
2	chr1:226391800-226397200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:226394800-226402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:226395000-226398000	Weak transcription	Spleen	Spleen
5	chr1:226395800-226397600	Bivalent Enhancer	HepG2	liver
6	chr1:226396200-226399600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:226396400-226397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:226396800-226397400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:226397000-226397200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:226397000-226397400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:226397000-226397600	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:226397000-226397600	Enhancers	Fetal Muscle Leg	muscle
13	chr1:226397000-226399200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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