Variant report

Variant	rs5754189
Chromosome Location	chr22:33048338-33048339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1012366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][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]
rs131069	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs3788470	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788472	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs3827337	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4303813	0.84[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4373007	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4821081	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5749479	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749480	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5754185	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5754186	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5754188	0.89[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5754190	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5754222	0.81[TSI][hapmap]
rs717168	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762899	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055541	chr22:33006967-33101138	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2762119	chr22:33006967-33101150	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1061824	chr22:33013014-33101138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv459875	chr22:33025180-33097662	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv588896	chr22:33025180-33097662	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5754189	PISD	cis	cerebellum	SCAN
rs5754189	TBC1D10A	cis	parietal	SCAN
rs5754189	HSCB	cis	parietal	SCAN
rs5754189	EIF4ENIF1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33040800-33053400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:33040800-33054400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:33041800-33050000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr22:33047000-33052000	Weak transcription	NHDF-Ad	bronchial
5	chr22:33047200-33051800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr22:33047200-33056400	Weak transcription	HSMM	muscle
7	chr22:33047400-33048600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:33047400-33048600	Weak transcription	Fetal Muscle Leg	muscle
9	chr22:33047400-33050400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr22:33047400-33052000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr22:33047600-33048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr22:33047800-33050400	Weak transcription	K562	blood
13	chr22:33047800-33051000	Enhancers	Fetal Stomach	stomach
14	chr22:33048000-33049600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr22:33048200-33049000	Enhancers	Fetal Muscle Trunk	muscle
16	chr22:33048200-33050800	Enhancers	Fetal Lung	lung

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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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