Variant report

Variant	rs4128763
Chromosome Location	chr9:99965768-99965769
allele	C/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	POLR2A	chr9:99965742-99966578	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ZNF322P1	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1048451	1.00[CEU][hapmap]
rs10521028	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10521029	1.00[CEU][hapmap]
rs10817491	1.00[CEU][hapmap]
rs10817504	0.88[CEU][hapmap]
rs10980890	0.92[EUR][1000 genomes]
rs10980955	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10980992	0.92[EUR][1000 genomes]
rs10981005	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981158	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981161	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10981297	1.00[CEU][hapmap]
rs10981367	1.00[CEU][hapmap]
rs10981460	1.00[CEU][hapmap]
rs10981784	1.00[CEU][hapmap]
rs10981800	1.00[CEU][hapmap]
rs11581	1.00[CEU][hapmap]
rs12377244	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12377538	1.00[CEU][hapmap]
rs12378350	1.00[CEU][hapmap]
rs12378555	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12550862	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12550923	1.00[CEU][hapmap]
rs12551740	1.00[CEU][hapmap]
rs12552659	1.00[CEU][hapmap]
rs12553213	1.00[CEU][hapmap]
rs12554363	1.00[CEU][hapmap]
rs12555277	1.00[CEU][hapmap]
rs13285567	0.92[CEU][hapmap]
rs13286510	1.00[CEU][hapmap]
rs13286601	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13287082	1.00[CEU][hapmap]
rs13287095	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13289134	1.00[CEU][hapmap]
rs13289813	1.00[CEU][hapmap]
rs13300328	1.00[CEU][hapmap]
rs13301045	1.00[CEU][hapmap]
rs1531440	0.94[CEU][hapmap]
rs1564048	1.00[CEU][hapmap]
rs16905669	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16919675	0.94[CEU][hapmap]
rs1857085	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1986462	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2045729	1.00[CEU][hapmap]
rs2045730	1.00[CEU][hapmap]
rs2045731	1.00[CEU][hapmap]
rs2306090	1.00[CEU][hapmap]
rs2306092	1.00[CEU][hapmap]
rs2306094	1.00[CEU][hapmap]
rs2401384	1.00[CEU][hapmap]
rs34592472	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34868501	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35241252	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35285539	0.96[EUR][1000 genomes]
rs3747490	1.00[CEU][hapmap]
rs3747491	1.00[CEU][hapmap]
rs3747492	1.00[CEU][hapmap]
rs3747495	1.00[CEU][hapmap]
rs3747498	1.00[CEU][hapmap]
rs3747499	1.00[CEU][hapmap]
rs3747504	1.00[CEU][hapmap]
rs3747506	0.94[CEU][hapmap]
rs3994560	1.00[CEU][hapmap]
rs4014782	0.91[EUR][1000 genomes]
rs4463540	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742688	1.00[CEU][hapmap]
rs4743061	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743062	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743070	1.00[CEU][hapmap]
rs4743073	1.00[CEU][hapmap]
rs4743082	1.00[CEU][hapmap]
rs4743083	1.00[CEU][hapmap]
rs4743085	1.00[CEU][hapmap]
rs4743086	1.00[CEU][hapmap]
rs56860287	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58003970	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7018753	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7020530	1.00[CEU][hapmap]
rs7021506	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7038496	1.00[CEU][hapmap]
rs7041222	1.00[CEU][hapmap]
rs7848439	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851025	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7860303	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7865758	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs898869	1.00[CEU][hapmap]
rs898870	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv972433	chr9:99962059-99983443	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4128763	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99961400-99968800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
2	chr9:99961400-99969200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr9:99961800-99968800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr9:99961800-99969000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
5	chr9:99961800-99969000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
6	chr9:99961800-99969000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr9:99962000-99967000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
8	chr9:99962400-99968800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
9	chr9:99962600-99967800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:99962600-99969000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
11	chr9:99963200-99965800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:99964400-99967200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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