Variant report

Variant	rs12422417
Chromosome Location	chr12:50764711-50764712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50742978..50745322-chr12:50762860..50765654,2	K562	blood:

Variant related genes	Relation type
ENSG00000185958	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10467106	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10506292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10783352	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783353	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876013	0.83[ASN][1000 genomes]
rs10876014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs10876015	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs10876016	0.89[ASN][1000 genomes]
rs10876017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs10876023	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876024	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10876027	0.92[EUR][1000 genomes]
rs10876028	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap]
rs11169331	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs11169332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs11169335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs11169339	0.87[ASN][1000 genomes]
rs11169345	0.89[ASN][1000 genomes]
rs11169347	0.89[ASN][1000 genomes]
rs11169348	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[ASN][1000 genomes]
rs11169349	0.89[ASN][1000 genomes]
rs11169350	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs11169357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169359	0.88[ASN][1000 genomes]
rs11169360	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169367	0.92[ASN][1000 genomes]
rs11169369	0.92[ASN][1000 genomes]
rs11169370	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs11169373	0.92[ASN][1000 genomes]
rs11169374	0.92[ASN][1000 genomes]
rs11169375	0.91[ASN][1000 genomes]
rs11169376	0.87[ASN][1000 genomes]
rs11169377	0.88[ASN][1000 genomes]
rs11169390	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169391	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169395	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833608	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11836169	0.92[ASN][1000 genomes]
rs11838347	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs12299669	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12299758	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312177	0.83[ASN][1000 genomes]
rs12367872	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12424691	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12424713	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs12424876	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425229	0.83[ASN][1000 genomes]
rs12425705	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][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[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821454	0.87[ASN][1000 genomes]
rs12823506	0.87[ASN][1000 genomes]
rs12828340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs12832940	0.89[ASN][1000 genomes]
rs1362983	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs17124562	0.83[ASN][1000 genomes]
rs1972611	0.87[ASN][1000 genomes]
rs2111988	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs2302900	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs2358539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs28628775	0.89[ASN][1000 genomes]
rs34039674	0.91[ASN][1000 genomes]
rs34614542	0.91[ASN][1000 genomes]
rs34825838	0.82[ASN][1000 genomes]
rs34849043	0.92[ASN][1000 genomes]
rs34858415	0.92[ASN][1000 genomes]
rs34894919	0.83[ASN][1000 genomes]
rs35209607	0.92[ASN][1000 genomes]
rs35535298	0.89[ASN][1000 genomes]
rs35768991	0.87[ASN][1000 genomes]
rs35878271	0.92[ASN][1000 genomes]
rs35933908	0.89[ASN][1000 genomes]
rs36017775	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812825	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.83[ASN][1000 genomes]
rs3861100	0.83[ASN][1000 genomes]
rs4348979	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4421818	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]
rs4445717	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768872	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768891	0.92[EUR][1000 genomes]
rs4768949	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768951	0.96[CEU][hapmap]
rs6580735	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	0.93[ASN][1000 genomes]
rs6580743	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs7134595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7135777	0.87[ASN][1000 genomes]
rs7138420	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7138622	0.96[CEU][hapmap]
rs7295847	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7296291	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301186	0.81[ASN][1000 genomes]
rs7301189	0.81[ASN][1000 genomes]
rs7302363	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304445	0.89[ASN][1000 genomes]
rs7305995	0.89[ASN][1000 genomes]
rs7308095	0.81[ASN][1000 genomes]
rs7310541	0.92[ASN][1000 genomes]
rs7311378	0.89[ASN][1000 genomes]
rs7311491	0.89[ASN][1000 genomes]
rs7311973	1.00[CEU][hapmap];0.89[ASN][1000 genomes]
rs7312252	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[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[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs7488682	0.89[ASN][1000 genomes]
rs7953953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs7956468	0.89[ASN][1000 genomes]
rs7971374	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7972824	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973243	0.81[EUR][1000 genomes]
rs7974648	0.86[ASN][1000 genomes]
rs7979830	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7980911	0.91[ASN][1000 genomes]
rs9668187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9705460	0.87[ASN][1000 genomes]
rs9739363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12422417	LASS5	cis	multi-tissue	Pritchard
rs12422417	DIP2B	cis	Lymphoblastoid	GTEx
rs12422417	FAIM2	cis	cerebellum	SCAN
rs12422417	KRT73	cis	parietal	SCAN
rs12422417	EPLIN	cis	multi-tissue	Pritchard
rs12422417	DIP2B	cis	multi-tissue	Pritchard
rs12422417	LASS5	cis	parietal	SCAN
rs12422417	LASS5	cis	cerebellum	SCAN
rs12422417	CELA1	cis	parietal	SCAN
rs12422417	SLC38A1	cis	parietal	SCAN
rs12422417	CERS5	cis	Nerve Tibial	GTEx
rs12422417	KIAA1463	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50764200-50764800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:50764600-50764800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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