Variant report

Variant	rs4682374
Chromosome Location	chr3:111942548-111942549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10511309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934138	0.90[ASN][1000 genomes]
rs10934158	0.81[ASN][1000 genomes]
rs1119338	0.83[ASN][1000 genomes]
rs11711153	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11712289	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11714145	0.81[ASN][1000 genomes]
rs11714273	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11715536	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11914637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11928353	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054138	0.88[ASN][1000 genomes]
rs12493824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494678	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12629465	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12634031	0.91[ASN][1000 genomes]
rs13060187	0.88[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.94[ASN][1000 genomes]
rs13064510	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13067030	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069887	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13079745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13088733	0.88[ASN][1000 genomes]
rs13314792	0.90[ASN][1000 genomes]
rs13314977	0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs13315900	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13327160	0.81[ASN][1000 genomes]
rs13327165	0.87[ASN][1000 genomes]
rs1586875	0.81[ASN][1000 genomes]
rs1602670	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1602671	0.83[ASN][1000 genomes]
rs1844995	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2029636	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2029637	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2046983	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2087767	0.86[ASN][1000 genomes]
rs2087768	0.86[ASN][1000 genomes]
rs2131233	0.98[ASN][1000 genomes]
rs2399405	0.83[ASN][1000 genomes]
rs3929356	0.91[ASN][1000 genomes]
rs4352358	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438629	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4440096	0.83[ASN][1000 genomes]
rs4528910	0.83[ASN][1000 genomes]
rs4568110	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4577433	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4586779	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4682361	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682365	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4682372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682379	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4682391	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs5013874	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs62277462	0.84[ASN][1000 genomes]
rs62279470	0.95[ASN][1000 genomes]
rs6438039	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438057	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6763462	0.84[ASN][1000 genomes]
rs6764064	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6764248	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6766122	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6766622	0.81[ASN][1000 genomes]
rs6766996	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767017	0.83[ASN][1000 genomes]
rs6768523	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs67704344	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773161	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6784524	0.91[ASN][1000 genomes]
rs6791042	0.83[ASN][1000 genomes]
rs6792318	0.80[ASN][1000 genomes]
rs6801501	0.83[ASN][1000 genomes]
rs6805795	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6807950	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6808920	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7611019	0.80[ASN][1000 genomes]
rs7614211	0.83[ASN][1000 genomes]
rs7616020	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7622733	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7642447	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7642496	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7646742	0.81[ASN][1000 genomes]
rs9288937	0.81[ASN][1000 genomes]
rs9288938	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9288943	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs958695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809174	0.87[JPT][hapmap]
rs9818716	0.98[ASN][1000 genomes]
rs9821935	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9827371	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9827793	0.83[ASN][1000 genomes]
rs9827894	0.90[ASN][1000 genomes]
rs9828290	0.83[ASN][1000 genomes]
rs9828502	0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs9837375	0.84[ASN][1000 genomes]
rs9844769	0.93[ASN][1000 genomes]
rs9859163	0.81[ASN][1000 genomes]
rs9861756	0.83[ASN][1000 genomes]
rs9864872	0.83[ASN][1000 genomes]
rs9871650	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9872691	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9875860	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591291	chr3:111914624-111962851	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
3	nsv591292	chr3:111914624-111993915	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	esv3437811	chr3:111929311-111950399	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
5	nsv877340	chr3:111936961-112013546	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4682374	CD200	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111937000-111942800	Weak transcription	Left Ventricle	heart
2	chr3:111942400-111952400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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