Variant report

Variant	rs6478020
Chromosome Location	chr9:99986704-99986705
allele	A/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	SP1	chr9:99986549-99986862	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99985067..99987314-chr9:99998375..100001266,2	K562	blood:

Variant related genes	Relation type
ANKRD18CP	TF binding region
ENSG00000254876	Chromatin interaction
ENSG00000254483	Chromatin interaction
ENSG00000197816	Chromatin interaction
ENSG00000203279	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10116019	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10119245	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10759522	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10817265	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981209	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10981280	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10981288	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10981296	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10981329	0.86[EUR][1000 genomes]
rs11562326	0.82[AMR][1000 genomes]
rs11791310	0.86[EUR][1000 genomes]
rs11794422	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11998999	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12004930	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12005128	0.80[EUR][1000 genomes]
rs12235734	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13297670	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13298346	0.86[EUR][1000 genomes]
rs13299029	0.81[AMR][1000 genomes]
rs13299627	0.80[EUR][1000 genomes]
rs13301357	0.84[EUR][1000 genomes]
rs28846196	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34382632	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3957904	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3994556	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4284138	0.86[EUR][1000 genomes]
rs4626726	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55694850	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022475	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7850392	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7850429	0.86[AMR][1000 genomes]
rs7850504	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7855366	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7855622	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7868440	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7868563	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7868806	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869509	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869568	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869587	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869959	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6478020	VN1R51P	cis	Thyroid	GTEx
rs6478020	ANKRD18CP	cis	Thyroid	GTEx
rs6478020	RP11-520B13.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99985200-99992000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:99985200-99995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:99985800-99994800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:99986200-99986800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
5	chr9:99986600-99994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links