Variant report

Variant	rs56860287
Chromosome Location	chr9:99936520-99936521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10521028	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10980890	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10980955	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10980992	0.95[EUR][1000 genomes]
rs10981005	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981158	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10981161	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12377244	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12378555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550862	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12555636	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13287095	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16905669	0.92[EUR][1000 genomes]
rs1857085	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986462	0.96[EUR][1000 genomes]
rs34592472	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34868501	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35241252	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35285539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4014782	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4128763	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4463540	0.86[EUR][1000 genomes]
rs4743061	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743062	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58003970	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018753	0.97[EUR][1000 genomes]
rs7020129	0.80[AMR][1000 genomes]
rs7021506	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7848439	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7851025	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860303	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7865758	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv972432	chr9:99874607-99958095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv415491	chr9:99933275-99937922	Strong transcription Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56860287	VN1R51P	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99911600-99957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:99918000-99946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:99921400-99948800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:99922000-99937800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:99923600-99938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:99932200-99936600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:99932800-99947200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:99934400-99951600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr9:99934400-99957800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:99934800-99957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:99936200-99936800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr9:99936200-99939800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:99936400-99936800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr9:99936400-99953200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links