Variant report

Variant	rs10981288
Chromosome Location	chr9:99996548-99996549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10116019	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10119245	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10122063	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10125198	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10435868	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10448274	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10759522	0.81[EUR][1000 genomes]
rs10817265	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10981209	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981296	0.87[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981329	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10981438	0.82[EUR][1000 genomes]
rs10981890	0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs11562326	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11581	0.86[JPT][hapmap]
rs11791310	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11794422	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11998999	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12004930	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005128	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12235305	0.82[EUR][1000 genomes]
rs12235734	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13297670	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13298346	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13299627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13301357	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13302699	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1544203	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1857083	0.87[AMR][1000 genomes]
rs1903635	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs1947717	0.86[ASW][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2169456	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2219664	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2242187	0.93[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2306097	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2374923	0.86[AMR][1000 genomes]
rs2493442	0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs2493443	0.81[EUR][1000 genomes]
rs2502644	0.86[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs2615143	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2615145	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2795365	0.81[EUR][1000 genomes]
rs2795367	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2818238	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2818239	0.81[EUR][1000 genomes]
rs2818243	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs28846196	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3214072	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs34382632	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34955252	0.81[EUR][1000 genomes]
rs35609998	0.82[EUR][1000 genomes]
rs3747489	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3747493	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3747496	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3957904	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3994556	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4014789	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4237189	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4284138	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4313271	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4366181	0.93[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4452918	0.84[AMR][1000 genomes]
rs4523384	0.81[EUR][1000 genomes]
rs4523385	0.81[ASW][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4626726	0.92[EUR][1000 genomes]
rs4743072	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4743076	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs4743077	0.93[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs4743084	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs55694850	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62556614	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6478020	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478095	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7020393	0.91[JPT][hapmap]
rs7022475	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7042707	0.91[JPT][hapmap]
rs713066	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs72747776	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7470446	0.81[EUR][1000 genomes]
rs750674	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7850392	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7850504	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7855366	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7855622	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7868440	0.82[EUR][1000 genomes]
rs7868563	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7868806	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869509	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869568	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869587	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869959	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10981288	LOC57653	cis	parietal	SCAN
rs10981288	HSD17B3	cis	parietal	SCAN
rs10981288	VN1R51P	cis	Thyroid	GTEx
rs10981288	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99992200-99999600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:99994600-99998200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:99994600-99998400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:99994800-99999000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:99995000-99998400	Weak transcription	Dnd41	blood
6	chr9:99995600-99999000	Weak transcription	HepG2	liver
7	chr9:99995600-99999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:99995600-99999800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr9:99995800-99997400	Weak transcription	K562	blood
10	chr9:99995800-99998200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:99995800-99998400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:99995800-99998400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:99995800-99999000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:99995800-99999600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:99995800-99999600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:99996000-99999000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:99996000-99999600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:99996200-99999200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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