Variant report

Variant	rs1573853
Chromosome Location	chr8:110663138-110663139
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr8:110663083-110663509	SH-SY5Y	brain:	n/a	chr8:110663313-110663329 chr8:110663316-110663326 chr8:110663318-110663335

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:110658808..110660979-chr8:110662720..110664457,2	K562	blood:
2	chr8:110656684..110658658-chr8:110660535..110663260,4	MCF-7	breast:

Variant related genes	Relation type
SYBU	TF binding region
ENSG00000147642	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10090145	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs10505131	0.85[JPT][hapmap]
rs10505132	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11774663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11998387	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13256586	0.97[ASN][1000 genomes]
rs13268243	0.89[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2702	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2844238	0.84[ASW][hapmap]
rs2844242	0.81[YRI][hapmap]
rs3108829	0.89[ASN][1000 genomes]
rs3108832	0.88[ASN][1000 genomes]
rs3108837	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3108840	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3108853	0.90[ASN][1000 genomes]
rs3108854	0.90[ASN][1000 genomes]
rs3108862	0.91[ASN][1000 genomes]
rs3108865	0.91[ASN][1000 genomes]
rs3108869	0.90[ASN][1000 genomes]
rs3133926	0.87[ASN][1000 genomes]
rs3133927	0.89[ASN][1000 genomes]
rs3133935	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133936	0.89[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3133937	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3134314	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3134317	0.91[ASN][1000 genomes]
rs3134319	0.91[ASN][1000 genomes]
rs3134325	0.89[ASN][1000 genomes]
rs3134331	0.89[ASN][1000 genomes]
rs4367512	0.88[ASW][hapmap];0.81[YRI][hapmap]
rs6469275	0.89[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6985646	0.99[ASN][1000 genomes]
rs7003380	0.81[YRI][hapmap]
rs7008447	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7813979	0.81[YRI][hapmap]

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	esv1849702	chr8:110594148-110683804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1573853	KCNV1	cis	lymphoblastoid	seeQTL
rs1573853	PKHD1L1	cis	Lymphoblastoid	GTEx
rs1573853	PKHD1L1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110661000-110664800	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links