Variant report

Variant	rs4421818
Chromosome Location	chr12:50749294-50749295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr12:50749264-50749381	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FAM186A	TF binding region

Extended variants
information (count: 140 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10467106	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10506292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10783352	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783353	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876013	0.83[ASN][1000 genomes]
rs10876014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10876015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs10876016	0.89[ASN][1000 genomes]
rs10876017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs10876023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10876027	0.91[EUR][1000 genomes]
rs10876028	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169314	0.80[ASN][1000 genomes]
rs11169315	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs11169317	0.81[ASN][1000 genomes]
rs11169319	0.80[ASN][1000 genomes]
rs11169322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11169331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11169332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11169335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs11169339	0.87[ASN][1000 genomes]
rs11169345	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169347	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[ASN][1000 genomes]
rs11169349	0.89[ASN][1000 genomes]
rs11169350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs11169357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169359	0.88[ASN][1000 genomes]
rs11169360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169367	0.92[ASN][1000 genomes]
rs11169369	0.92[ASN][1000 genomes]
rs11169370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11169373	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11169374	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11169375	0.91[ASN][1000 genomes]
rs11169376	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11169377	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11169390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169391	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169395	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833608	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[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]
rs11836169	0.92[ASN][1000 genomes]
rs11838347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12299669	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299758	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312177	0.83[ASN][1000 genomes]
rs12367872	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs12422417	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12424713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs12424876	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425229	0.83[ASN][1000 genomes]
rs12425705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12426444	0.88[ASN][1000 genomes]
rs12582180	0.90[EUR][1000 genomes]
rs12811291	0.83[ASN][1000 genomes]
rs12814094	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821454	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12823506	0.87[ASN][1000 genomes]
rs12828340	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs12832940	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1362983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs17124562	0.83[ASN][1000 genomes]
rs1972611	0.87[ASN][1000 genomes]
rs2111988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2302900	0.96[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs2358539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs28628775	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34039674	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34614542	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34825838	0.82[ASN][1000 genomes]
rs34849043	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34858415	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34894919	0.83[ASN][1000 genomes]
rs35209607	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35535298	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35768991	0.87[ASN][1000 genomes]
rs35878271	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35933908	0.89[ASN][1000 genomes]
rs36017775	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs3861100	0.83[ASN][1000 genomes]
rs4348979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445717	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768855	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768872	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768891	0.91[EUR][1000 genomes]
rs4768949	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768951	0.96[CEU][hapmap]
rs6580735	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6580736	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs6580737	0.89[ASN][1000 genomes]
rs6580738	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs6580739	0.91[ASN][1000 genomes]
rs6580741	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6580743	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs7134595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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]
rs7135777	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7138420	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7138622	0.96[CEU][hapmap]
rs7295847	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7296291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301186	0.81[ASN][1000 genomes]
rs7301189	0.81[ASN][1000 genomes]
rs7302363	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304445	0.89[ASN][1000 genomes]
rs7305995	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7308095	0.81[ASN][1000 genomes]
rs7310541	0.92[ASN][1000 genomes]
rs7311378	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7311491	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7311973	1.00[CEU][hapmap];0.89[ASN][1000 genomes]
rs7312252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315690	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7315955	0.87[ASN][1000 genomes]
rs7486747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[LWK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs7488682	0.89[ASN][1000 genomes]
rs7953953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs7956468	0.89[ASN][1000 genomes]
rs7971374	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7972824	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973243	0.82[EUR][1000 genomes]
rs7974648	0.86[ASN][1000 genomes]
rs7979830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs7980911	0.91[ASN][1000 genomes]
rs9668187	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9705460	0.87[ASN][1000 genomes]
rs9739363	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4421818	ATF1	cis	Artery Tibial	GTEx
rs4421818	EPLIN	cis	multi-tissue	Pritchard
rs4421818	FAIM2	cis	cerebellum	SCAN
rs4421818	LASS5	cis	cerebellum	SCAN
rs4421818	LASS5	cis	multi-tissue	Pritchard
rs4421818	CERS5	cis	Nerve Tibial	GTEx
rs4421818	KIAA1463	cis	multi-tissue	Pritchard
rs4421818	KRT73	cis	parietal	SCAN
rs4421818	CELA1	cis	parietal	SCAN
rs4421818	POU6F1	cis	lymphoblastoid	seeQTL
rs4421818	DIP2B	cis	multi-tissue	Pritchard
rs4421818	SLC38A1	cis	parietal	SCAN
rs4421818	DIP2B	cis	Lymphoblastoid	GTEx
rs4421818	LASS5	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50747000-50749400	Enhancers	HepG2	liver
2	chr12:50748000-50751800	Weak transcription	Left Ventricle	heart
3	chr12:50748200-50752000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:50749200-50753400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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