Variant report

Variant	rs4452918
Chromosome Location	chr9:99929723-99929724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10119245	0.80[EUR][1000 genomes]
rs10122063	0.91[JPT][hapmap]
rs10125198	0.86[JPT][hapmap]
rs10435868	0.91[JPT][hapmap]
rs10448274	0.91[JPT][hapmap]
rs10817170	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10817171	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10817173	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10980874	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981209	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10981280	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs10981288	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs10981296	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs10981329	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs11562326	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11791310	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs11998999	0.81[AMR][1000 genomes]
rs12003313	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12004930	0.81[AMR][1000 genomes]
rs12235734	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13297670	0.81[AMR][1000 genomes]
rs13298346	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs13299627	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1544203	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs1857083	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1947717	0.80[JPT][hapmap]
rs2219664	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs2306097	0.91[JPT][hapmap]
rs2374923	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2615143	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs2615145	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs2795367	0.88[CEU][hapmap]
rs2818238	0.92[CEU][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs2818243	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs3214072	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs34382632	0.80[AMR][1000 genomes]
rs35988269	0.84[EUR][1000 genomes]
rs3747496	0.86[JPT][hapmap]
rs3862336	0.82[ASN][1000 genomes]
rs4014783	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4014789	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4145255	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4237189	0.91[JPT][hapmap]
rs4313271	0.86[JPT][hapmap]
rs4743072	0.85[CEU][hapmap];0.91[JPT][hapmap]
rs4743076	0.86[JPT][hapmap]
rs4743077	0.86[JPT][hapmap]
rs55694850	0.81[AMR][1000 genomes]
rs62556614	0.82[EUR][1000 genomes]
rs6478095	0.91[JPT][hapmap]
rs7020393	0.81[JPT][hapmap]
rs7031789	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7042707	0.81[JPT][hapmap]
rs713066	0.87[CEU][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs750674	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs7863123	0.83[ASN][1000 genomes]
rs7869959	0.84[EUR][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	nsv969696	chr9:99928429-99933157	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4452918	VN1R51P	cis	Thyroid	GTEx
rs4452918	LOC57653	cis	parietal	SCAN
rs4452918	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:17 , 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	chr9:99913400-99930800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:99913600-99930800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:99918000-99946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:99921400-99948800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:99922000-99937800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:99923600-99932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:99923600-99938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:99923800-99936200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:99925800-99930200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:99926000-99933000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:99926000-99933000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:99927400-99930200	Weak transcription	K562	blood
14	chr9:99927400-99934400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:99929000-99930800	Enhancers	GM12878-XiMat	blood
16	chr9:99929000-99931400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:99929400-99932000	Enhancers	Dnd41	blood

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