Variant report

Variant	rs10008069
Chromosome Location	chr4:79605287-79605288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79602819..79606934-chr4:79608237..79614104,8	K562	blood:
2	chr4:79603993..79609685-chr4:79610850..79614972,9	K562	blood:
3	chr4:79604157..79606755-chr4:79612814..79614519,2	MCF-7	breast:
4	chr4:79603191..79606883-chr4:79607148..79610716,4	K562	blood:
5	chr4:79598044..79600177-chr4:79603661..79605687,2	MCF-7	breast:
6	chr4:79604462..79605994-chr4:79695517..79698209,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANXA3-1	chr4:79601915-79605655	NONHSAT097070
2	lnc-ANXA3-1	chr4:79601915-79605655	NONHSAT097071
3	lnc-ANXA3-1	chr4:79601915-79605655	NONHSAT097072
4	lnc-ANXA3-1	chr4:79601915-79605655	NONHSAT097073
5	lnc-ANXA3-1	chr4:79601915-79605655	NONHSAT097074
6	lnc-ANXA3-1	chr4:79601915-79605655	NONHSAT097075

No data

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10008008	0.86[EUR][1000 genomes]
rs10028815	0.87[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs10029214	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs1134123	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1134124	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11724233	0.80[CHB][hapmap]
rs12510411	0.91[CEU][hapmap]
rs12639656	0.92[CEU][hapmap]
rs12711028	0.85[CEU][hapmap]
rs13110339	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs13133277	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1346144	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1346145	0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1532427	0.92[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1806906	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1834519	0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2867465	0.87[EUR][1000 genomes]
rs2867466	0.87[EUR][1000 genomes]
rs4074675	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4254805	0.92[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs4257676	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264856	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4321658	0.90[EUR][1000 genomes]
rs4365753	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4472162	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs4472163	0.85[CHB][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4495064	0.91[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs4560439	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4612	0.91[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs4619914	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533828	0.80[AMR][1000 genomes]
rs6533940	0.87[EUR][1000 genomes]
rs6533951	0.80[CHB][hapmap]
rs6815367	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818230	0.87[EUR][1000 genomes]
rs6825593	0.82[EUR][1000 genomes]
rs6842686	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs6842723	0.92[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs6855458	0.87[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7672208	0.82[EUR][1000 genomes]
rs7675646	0.92[CEU][hapmap]
rs7677162	0.82[EUR][1000 genomes]
rs7677783	0.90[CEU][hapmap];0.89[JPT][hapmap]
rs7694971	0.82[EUR][1000 genomes]
rs7699519	0.82[EUR][1000 genomes]
rs7699905	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9992088	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10008069	USO1	cis	parietal	SCAN
rs10008069	LOC643424	cis	multi-tissue	Pritchard
rs10008069	ANXA3	cis	cerebellum	SCAN
rs10008069	CXCL10	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79599200-79605400	Weak transcription	Small Intestine	intestine
2	chr4:79604000-79605600	Enhancers	K562	blood
3	chr4:79604200-79610000	Weak transcription	Fetal Intestine Large	intestine
4	chr4:79604600-79606200	Enhancers	NHLF	lung
5	chr4:79604600-79606600	Enhancers	HSMM	muscle
6	chr4:79604800-79605400	Enhancers	Fetal Heart	heart
7	chr4:79604800-79606000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr4:79604800-79606600	Enhancers	HSMMtube	muscle
9	chr4:79604800-79606600	Enhancers	NHDF-Ad	bronchial
10	chr4:79605000-79605400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:79605000-79605600	Enhancers	A549	lung
12	chr4:79605000-79606000	Enhancers	NH-A	brain
13	chr4:79605000-79606200	Enhancers	HUVEC	blood vessel
14	chr4:79605200-79605600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:79605200-79605600	Enhancers	Placenta	Placenta
16	chr4:79605200-79605800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:79605200-79605800	Enhancers	Fetal Intestine Small	intestine
18	chr4:79605200-79605800	Enhancers	NHEK	skin
19	chr4:79605200-79606000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:79605200-79606000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:79605200-79606000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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