Variant report

Variant	rs2227543
Chromosome Location	chr4:74607910-74607911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10005565	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10009462	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10009488	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10010970	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10012962	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10015626	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10019318	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10031141	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10938092	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938094	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10938095	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10938096	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938097	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10938100	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10938101	0.82[EUR][1000 genomes]
rs1126647	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730284	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11730560	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730667	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733222	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11938389	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13106097	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13109377	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13112910	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13116536	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13117876	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16849928	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16849945	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16849958	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1951236	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1951240	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1951242	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1957070	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1957661	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2145617	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap]
rs2224434	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap]
rs2227306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2227307	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2227521	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2367276	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28609798	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28612337	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28833215	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2886920	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2886922	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4073	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4279174	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4549349	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4694178	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4694636	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4694637	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62312370	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6446959	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446960	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6446961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6820848	0.81[EUR][1000 genomes]
rs6831029	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6851997	0.83[EUR][1000 genomes]
rs6853679	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7689435	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9999262	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999446	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012198	chr4:74487793-74621952	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv537139	chr4:74487793-74621952	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1005231	chr4:74555497-74680079	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv980219	chr4:74603561-74618789	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2227543	PF4V1	cis	multi-tissue	Pritchard
rs2227543	SCARB2	cis	parietal	SCAN
rs2227543	ALB	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74606200-74608000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:74606200-74608400	Active TSS	Primary B cells from cord blood	blood
3	chr4:74606200-74610200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:74606400-74609400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:74606400-74616800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:74606800-74610400	Weak transcription	NH-A	brain
7	chr4:74607200-74610600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:74607400-74608000	Active TSS	Muscle Satellite Cultured Cells	--
9	chr4:74607400-74608000	Enhancers	Hela-S3	cervix
10	chr4:74607400-74608800	Enhancers	HUVEC	blood vessel
11	chr4:74607400-74613400	Weak transcription	NHEK	skin
12	chr4:74607400-74616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:74607600-74608200	Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:74607600-74610600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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