Variant report

Variant	rs10773152
Chromosome Location	chr12:122910180-122910181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10161534	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10734915	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10734918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734924	0.88[JPT][hapmap];0.83[TSI][hapmap]
rs10744192	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744208	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744209	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744210	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744211	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744217	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744220	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10744287	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10773075	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10773088	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10773103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773104	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773167	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773172	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10773176	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773178	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773208	0.85[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846664	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10846688	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846764	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846792	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846826	0.95[AMR][1000 genomes]
rs10846830	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846835	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10846920	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846921	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846931	0.85[EUR][1000 genomes]
rs10846978	0.85[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs10847179	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10847242	0.88[JPT][hapmap]
rs10998	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap]
rs11057786	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11057797	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057882	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11058034	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11058209	0.84[EUR][1000 genomes]
rs11058226	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058233	0.86[EUR][1000 genomes]
rs11058251	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11058282	0.82[EUR][1000 genomes]
rs11058402	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11616082	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11836188	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12369858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs12372756	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12423420	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12425970	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12581249	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1473553	0.85[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs1553179	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1803290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1818050	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1973463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062488	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2173582	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2341439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28730465	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34129612	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817011	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4039670	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4319547	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4758643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758644	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758645	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4758646	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758662	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997380	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs55834409	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488933	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488939	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488951	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488958	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489002	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489156	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6489157	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7135419	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294559	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301515	0.84[CEU][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs7307735	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7314638	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7316114	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7397299	0.84[EUR][1000 genomes]
rs7398014	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952868	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7953007	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7956480	1.00[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7964138	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969429	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7973869	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7974262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975747	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9705654	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs9788145	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988963	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10773152	B3GNT4	cis	cerebellum	SCAN
rs10773152	GATC	cis	cerebellum	SCAN
rs10773152	RNF34	cis	parietal	SCAN
rs10773152	NME2P1	cis	cerebellum	SCAN
rs10773152	GTF2H3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122908200-122910600	Enhancers	Primary B cells from cord blood	blood
2	chr12:122908400-122910600	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:122908400-122922000	Weak transcription	Right Atrium	heart
4	chr12:122908600-122910400	Enhancers	HepG2	liver
5	chr12:122908600-122910800	Weak transcription	Thymus	Thymus
6	chr12:122908600-122916000	Weak transcription	Liver	Liver
7	chr12:122908800-122911800	Weak transcription	Placenta	Placenta
8	chr12:122908800-122919000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:122908800-122921800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:122909600-122910200	Enhancers	Pancreas	Pancrea
11	chr12:122909600-122910400	Enhancers	A549	lung
12	chr12:122909800-122910200	Weak transcription	GM12878-XiMat	blood
13	chr12:122910000-122910200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:122910000-122910200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:122910000-122910200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:122910000-122910400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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