Variant report

Variant	rs12646327
Chromosome Location	chr4:69941024-69941025
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs10006452	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10021748	0.91[CHB][hapmap]
rs11249521	0.82[EUR][1000 genomes]
rs11249522	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249523	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11249524	0.82[EUR][1000 genomes]
rs11249525	0.85[CEU][hapmap]
rs11249526	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11249527	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11249528	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11931182	0.83[EUR][1000 genomes]
rs11932131	0.82[EUR][1000 genomes]
rs11934762	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11935886	0.80[EUR][1000 genomes]
rs11940220	0.81[EUR][1000 genomes]
rs11940316	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12506962	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12508257	0.81[EUR][1000 genomes]
rs12512526	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12513195	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12642938	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12643840	0.82[EUR][1000 genomes]
rs12647434	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12647681	0.81[EUR][1000 genomes]
rs12647682	0.81[EUR][1000 genomes]
rs12648830	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs13140844	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs13147648	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs1902929	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs28375964	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28712409	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34318523	0.81[EUR][1000 genomes]
rs34386959	0.81[EUR][1000 genomes]
rs34630750	0.81[EUR][1000 genomes]
rs35297888	0.82[EUR][1000 genomes]
rs3922514	0.91[CHB][hapmap]
rs3924192	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4131317	0.82[EUR][1000 genomes]
rs4235108	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs4235111	0.81[CHB][hapmap]
rs4273534	0.82[EUR][1000 genomes]
rs4274916	0.85[CEU][hapmap]
rs4293848	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4299666	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs4305590	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs4307027	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4309908	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4314345	0.80[EUR][1000 genomes]
rs4318715	0.85[CEU][hapmap]
rs4327554	0.85[CEU][hapmap]
rs4337789	0.81[EUR][1000 genomes]
rs4351080	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4353969	0.81[CHB][hapmap]
rs4356974	0.81[EUR][1000 genomes]
rs4364327	0.80[EUR][1000 genomes]
rs4371687	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4371688	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4377650	0.81[CHB][hapmap]
rs4400060	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4400061	0.91[CHB][hapmap]
rs4413468	0.90[CHB][hapmap]
rs4440295	0.85[CHD][hapmap]
rs4443355	0.82[EUR][1000 genomes]
rs4446390	0.91[CHB][hapmap]
rs4446391	0.81[EUR][1000 genomes]
rs4454000	0.82[EUR][1000 genomes]
rs4455491	0.81[EUR][1000 genomes]
rs4458521	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4478248	0.82[EUR][1000 genomes]
rs4495114	0.81[CHB][hapmap]
rs4516790	0.87[ASN][1000 genomes]
rs4521414	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4522933	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4535394	0.85[CEU][hapmap]
rs4540108	0.82[EUR][1000 genomes]
rs4541594	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4554144	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4576082	0.81[JPT][hapmap]
rs4587017	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4588522	0.80[EUR][1000 genomes]
rs4600986	0.81[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap]
rs4632729	0.82[EUR][1000 genomes]
rs4640729	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4642304	0.82[EUR][1000 genomes]
rs4694169	0.96[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4694171	0.82[EUR][1000 genomes]
rs4694591	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4694596	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694603	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694610	0.91[CHB][hapmap]
rs5013211	0.81[EUR][1000 genomes]
rs55757747	0.82[EUR][1000 genomes]
rs55834557	0.81[EUR][1000 genomes]
rs56217918	0.82[EUR][1000 genomes]
rs56388229	0.80[EUR][1000 genomes]
rs57216626	0.80[EUR][1000 genomes]
rs58544196	0.81[EUR][1000 genomes]
rs59415892	0.81[EUR][1000 genomes]
rs62296922	0.82[EUR][1000 genomes]
rs62296935	0.82[EUR][1000 genomes]
rs62296936	0.82[EUR][1000 genomes]
rs62296942	0.81[EUR][1000 genomes]
rs62296943	0.81[EUR][1000 genomes]
rs62296944	0.81[EUR][1000 genomes]
rs6422323	0.96[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6422324	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6422325	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6600866	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6600874	0.82[EUR][1000 genomes]
rs6600875	0.82[EUR][1000 genomes]
rs6600876	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6600877	0.82[EUR][1000 genomes]
rs6600878	0.81[EUR][1000 genomes]
rs6600879	0.81[EUR][1000 genomes]
rs6600880	0.81[EUR][1000 genomes]
rs6600883	0.81[EUR][1000 genomes]
rs6600884	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6600885	0.81[EUR][1000 genomes]
rs6600886	0.81[EUR][1000 genomes]
rs6600887	0.81[EUR][1000 genomes]
rs6600888	0.81[EUR][1000 genomes]
rs6600890	0.81[EUR][1000 genomes]
rs6600891	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6600893	0.85[CEU][hapmap]
rs6600897	0.85[CEU][hapmap]
rs6600898	0.85[CEU][hapmap]
rs6820734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6827511	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs6830368	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6843382	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6846298	0.82[EUR][1000 genomes]
rs6851282	0.81[EUR][1000 genomes]
rs6851533	0.85[CEU][hapmap]
rs6858558	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7375178	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7434332	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7437039	0.81[EUR][1000 genomes]
rs7437174	0.82[EUR][1000 genomes]
rs7438033	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs7438135	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7438244	0.81[EUR][1000 genomes]
rs7438808	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs7439098	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7439152	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7439326	0.81[EUR][1000 genomes]
rs7439366	0.85[CEU][hapmap]
rs7439792	0.81[EUR][1000 genomes]
rs7441736	0.80[CHB][hapmap]
rs7441750	0.80[EUR][1000 genomes]
rs7441774	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7442453	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7442486	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7657423	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7657426	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs7659306	0.82[EUR][1000 genomes]
rs7662029	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7662632	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs7663584	0.82[EUR][1000 genomes]
rs7668258	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7674851	0.82[EUR][1000 genomes]
rs7676472	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7677611	0.82[EUR][1000 genomes]
rs7678656	0.81[EUR][1000 genomes]
rs7679184	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7679550	0.82[EUR][1000 genomes]
rs7680709	0.82[EUR][1000 genomes]
rs7681790	0.85[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7698645	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7698846	0.81[EUR][1000 genomes]
rs7699711	0.83[EUR][1000 genomes]
rs7699955	0.95[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9999076	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv594583	chr4:69928642-69988378	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv427683	chr4:69929701-70414172	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv522091	chr4:69932587-69988378	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv999858	chr4:69933262-70676525	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12646327	UGT2B28	cis	multi-tissue	Pritchard
rs12646327	UGT2B7	cis	multi-tissue	Pritchard
rs12646327	UTP3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69930600-69944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:69938800-69957400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:69940000-69941200	Enhancers	Liver	Liver
4	chr4:69940800-69941200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:69940800-69941800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr4:69941000-69941400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:69941000-69941400	Enhancers	A549	lung
8	chr4:69941000-69941600	Enhancers	Muscle Satellite Cultured Cells	--

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