Variant report

Variant	rs10980992
Chromosome Location	chr9:99946041-99946042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1048451	0.89[CEU][hapmap]
rs10521028	0.95[EUR][1000 genomes]
rs10521029	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs10817491	0.89[CEU][hapmap]
rs10980890	0.90[EUR][1000 genomes]
rs10980955	0.95[EUR][1000 genomes]
rs10981005	0.94[EUR][1000 genomes]
rs10981158	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10981161	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10981297	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs10981367	0.87[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs10981460	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs10981784	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs10981800	0.89[CEU][hapmap]
rs11581	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs12377244	0.89[EUR][1000 genomes]
rs12377538	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs12378350	0.87[ASW][hapmap];0.89[CEU][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs12378555	0.95[EUR][1000 genomes]
rs12550862	0.92[EUR][1000 genomes]
rs12550923	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs12551740	0.89[CEU][hapmap]
rs12552659	0.87[CEU][hapmap];0.82[YRI][hapmap]
rs12553213	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs12554363	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs13286510	0.89[CEU][hapmap]
rs13287082	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs13287095	0.83[EUR][1000 genomes]
rs13289134	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs13289813	0.88[CEU][hapmap]
rs13300328	0.88[CEU][hapmap]
rs13301045	0.93[CEU][hapmap]
rs1564048	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs16905669	0.88[EUR][1000 genomes]
rs1857085	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1986462	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs2045729	0.87[ASW][hapmap];0.89[CEU][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap]
rs2045730	0.89[CEU][hapmap]
rs2045731	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs2290933	0.83[YRI][hapmap]
rs2306090	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs2306092	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs2306094	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs2401384	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs34592472	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34868501	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs35241252	0.89[EUR][1000 genomes]
rs35285539	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3747490	0.89[CEU][hapmap]
rs3747491	0.89[CEU][hapmap]
rs3747492	0.89[CEU][hapmap]
rs3747495	0.87[ASW][hapmap];0.89[CEU][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs3747498	0.89[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs3747499	0.87[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs3747504	0.89[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap]
rs3747506	0.87[ASW][hapmap];0.83[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs3994560	0.87[ASW][hapmap];0.89[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs4014782	0.91[EUR][1000 genomes]
rs4128763	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs4463540	0.81[EUR][1000 genomes]
rs4742688	0.89[CEU][hapmap]
rs4743061	0.89[EUR][1000 genomes]
rs4743062	0.89[EUR][1000 genomes]
rs4743070	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs4743073	0.89[CEU][hapmap]
rs4743082	0.87[ASW][hapmap];0.89[CEU][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs4743083	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs56860287	0.95[EUR][1000 genomes]
rs58003970	0.95[EUR][1000 genomes]
rs7018753	0.92[EUR][1000 genomes]
rs7020530	0.89[CEU][hapmap]
rs7021506	0.89[EUR][1000 genomes]
rs7038496	0.89[CEU][hapmap]
rs7041222	0.88[CEU][hapmap]
rs7848439	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7851025	0.95[EUR][1000 genomes]
rs7860303	0.94[EUR][1000 genomes]
rs7865758	0.95[EUR][1000 genomes]
rs898869	0.89[CEU][hapmap];0.96[TSI][hapmap]
rs898870	0.89[CEU][hapmap];0.96[TSI][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	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
2	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
3	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10980992	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	chr9:99932800-99947200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:99934400-99951600	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr9:99934400-99957800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:99934800-99957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:99936400-99953200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:99936600-99957600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:99936800-99951800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:99942000-99951200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:99942800-99962600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:99945800-99947200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:99946000-99948000	Weak transcription	H9 Cell Line	embryonic stem cell

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