Variant report

Variant	rs4744451
Chromosome Location	chr9:98023305-98023306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10115247	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1045276	0.81[JPT][hapmap]
rs10491560	0.81[JPT][hapmap]
rs10739992	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739993	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10761377	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10761382	0.85[CEU][hapmap]
rs10821451	0.81[EUR][1000 genomes]
rs10821453	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821454	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821455	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10993490	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13295862	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs171417	0.90[JPT][hapmap]
rs17686583	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184818	0.90[JPT][hapmap]
rs1979022	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2031599	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2166402	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2282216	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2297596	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297597	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2404457	0.85[EUR][1000 genomes]
rs3277	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34045846	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34532504	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs356666	0.90[JPT][hapmap]
rs356673	0.90[JPT][hapmap]
rs356675	0.90[JPT][hapmap]
rs356677	0.90[JPT][hapmap]
rs356678	0.90[JPT][hapmap]
rs356680	0.90[JPT][hapmap]
rs356684	0.90[JPT][hapmap]
rs356689	0.90[JPT][hapmap]
rs3737142	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780561	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3780562	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3780564	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3780567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3780568	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3824486	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3844341	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3852402	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs416792	0.90[JPT][hapmap]
rs4647376	0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4647382	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4647443	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647459	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647462	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4647475	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647528	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4647529	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647534	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4647554	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4647558	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4744446	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744454	0.85[EUR][1000 genomes]
rs540412	0.81[JPT][hapmap]
rs565293	0.90[JPT][hapmap]
rs6479601	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7019043	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023007	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7027204	0.96[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7033633	0.81[JPT][hapmap]
rs7034538	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7850958	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7854570	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7872648	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7874310	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs879492	0.84[EUR][1000 genomes]
rs881791	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs944934	0.81[JPT][hapmap]
rs963774	0.96[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4744451	LOC57653	cis	cerebellum	SCAN
rs4744451	SYK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97973600-98024000	Weak transcription	Gastric	stomach
2	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:98007400-98024000	Weak transcription	Small Intestine	intestine
4	chr9:98009000-98026600	Weak transcription	A549	lung
5	chr9:98009200-98027600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:98009600-98023800	Weak transcription	Fetal Intestine Large	intestine
7	chr9:98013200-98025400	Weak transcription	Ovary	ovary
8	chr9:98013200-98027400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:98013400-98024600	Weak transcription	Right Ventricle	heart
10	chr9:98013400-98027600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:98015600-98027600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:98017600-98030800	Weak transcription	Fetal Stomach	stomach

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