Variant report

Variant	rs1806906
Chromosome Location	chr4:79603920-79603921
allele	C/T
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:4)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79602819..79606934-chr4:79608237..79614104,8	K562	blood:
2	chr4:79603191..79606883-chr4:79607148..79610716,4	K562	blood:
3	chr4:79598044..79600177-chr4:79603661..79605687,2	MCF-7	breast:
4	chr4:79603223..79604986-chr4:79695668..79697627,2	K562	blood:

(count:7 , 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
7	lnc-ANXA3-1	chr4:79601913-79604339	NONHSAT097076

No data

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10008008	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008069	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]
rs10028815	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]
rs10029214	0.88[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs1134123	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134124	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510411	0.87[CEU][hapmap]
rs12639656	0.88[CEU][hapmap]
rs12711028	0.81[CEU][hapmap]
rs13110339	0.86[CEU][hapmap]
rs13133277	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1346144	0.84[EUR][1000 genomes]
rs1346145	0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1532427	0.88[CEU][hapmap]
rs1834519	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867465	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867466	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4074675	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4254805	0.88[CEU][hapmap]
rs4257676	0.90[EUR][1000 genomes]
rs4264856	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4321658	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4365753	0.80[CEU][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs4472162	0.82[EUR][1000 genomes]
rs4472163	0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4495064	0.87[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs4560439	0.80[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4612	0.87[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs4619914	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs6533940	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815367	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6818230	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6825593	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6842686	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs6842723	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs6855458	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7672208	0.82[EUR][1000 genomes]
rs7675646	0.88[CEU][hapmap]
rs7677162	0.82[EUR][1000 genomes]
rs7677783	0.86[CEU][hapmap]
rs7694971	0.82[EUR][1000 genomes]
rs7699519	0.82[EUR][1000 genomes]
rs7699905	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9992088	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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
rs1806906	LOC643424	cis	multi-tissue	Pritchard
rs1806906	CXCL10	cis	parietal	SCAN
rs1806906	ANXA3	cis	cerebellum	SCAN
rs1806906	USO1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79599200-79605400	Weak transcription	Small Intestine	intestine
2	chr4:79602200-79604000	Weak transcription	K562	blood
3	chr4:79602600-79604200	Enhancers	Fetal Intestine Large	intestine
4	chr4:79602800-79604200	Enhancers	Duodenum Mucosa	Duodenum
5	chr4:79603000-79604200	Enhancers	Fetal Intestine Small	intestine
6	chr4:79603200-79604800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links