Variant report

Variant	rs4446571
Chromosome Location	chr6:45257662-45257663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 228 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:224)

rs_ID	r²[population]
rs10456552	0.97[ASN][1000 genomes]
rs1080415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10807318	0.85[ASN][1000 genomes]
rs10807319	0.89[ASN][1000 genomes]
rs10807320	0.90[ASN][1000 genomes]
rs10948222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948225	0.85[ASN][1000 genomes]
rs10948227	0.85[ASN][1000 genomes]
rs10948228	0.85[ASN][1000 genomes]
rs10948229	0.98[ASN][1000 genomes]
rs10948230	0.84[ASN][1000 genomes]
rs12194311	0.95[ASN][1000 genomes]
rs12199720	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12205274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12205312	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12208924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12524270	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs12524323	0.98[ASN][1000 genomes]
rs12525603	0.85[ASN][1000 genomes]
rs12526462	0.84[ASN][1000 genomes]
rs12526484	0.85[ASN][1000 genomes]
rs12527586	0.85[ASN][1000 genomes]
rs12529295	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs12529946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12530207	0.89[JPT][hapmap]
rs12662272	0.89[JPT][hapmap]
rs12662664	0.85[ASN][1000 genomes]
rs12662685	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs12663469	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1284955	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1284961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1284962	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1284964	0.89[JPT][hapmap]
rs1284965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1284967	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1284969	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1284972	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1284973	0.80[ASN][1000 genomes]
rs1284975	0.80[ASN][1000 genomes]
rs1284986	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1284987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1284988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1284992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1284999	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1285004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1285005	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1285007	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1285009	0.89[JPT][hapmap]
rs1285011	0.89[JPT][hapmap]
rs1285013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1285014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1285019	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1285022	0.81[ASN][1000 genomes]
rs1285023	0.81[ASN][1000 genomes]
rs1285026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1285029	0.89[JPT][hapmap]
rs1285030	0.81[CHB][hapmap]
rs1285033	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1290386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1300126	0.80[ASN][1000 genomes]
rs1304168	0.87[ASN][1000 genomes]
rs1321081	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1324530	0.89[JPT][hapmap]
rs1324532	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1324535	0.89[JPT][hapmap]
rs1324537	0.80[ASN][1000 genomes]
rs1324540	0.88[ASN][1000 genomes]
rs1359336	0.82[ASN][1000 genomes]
rs1406848	0.80[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1555681	0.88[CEU][hapmap]
rs1581777	0.89[ASN][1000 genomes]
rs1629542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16873257	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs16873345	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs16873348	0.80[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs16873364	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs16873366	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs16873373	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs16873379	0.80[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs17288278	0.98[ASN][1000 genomes]
rs1748231	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1748233	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs1748234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1748235	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1748238	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1748240	0.89[JPT][hapmap]
rs1748242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1797145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1852985	0.83[ASN][1000 genomes]
rs1852986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1886345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2024786	0.80[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2024787	0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2057552	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs2057553	0.89[JPT][hapmap]
rs2093901	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2093903	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2295295	0.84[ASN][1000 genomes]
rs2295296	0.84[ASN][1000 genomes]
rs2396425	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2396502	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2396504	0.97[ASN][1000 genomes]
rs2815263	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs28360524	0.85[ASN][1000 genomes]
rs34677014	0.85[ASN][1000 genomes]
rs3749863	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs3763190	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3923353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4236086	0.85[ASN][1000 genomes]
rs4312985	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs4339452	0.80[ASN][1000 genomes]
rs4341001	0.85[ASN][1000 genomes]
rs4352679	0.90[ASN][1000 genomes]
rs4373351	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];0.96[ASN][1000 genomes]
rs4401652	0.85[ASN][1000 genomes]
rs4463250	0.85[ASN][1000 genomes]
rs4506035	0.89[EUR][1000 genomes]
rs4510673	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4521587	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs4590263	0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4610549	0.83[ASN][1000 genomes]
rs4631280	0.88[EUR][1000 genomes]
rs4711813	0.85[ASN][1000 genomes]
rs4711814	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4714845	0.87[ASN][1000 genomes]
rs4714847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4714848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4714850	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4714853	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs55959525	0.80[ASN][1000 genomes]
rs56243649	0.85[ASN][1000 genomes]
rs58100797	0.81[ASN][1000 genomes]
rs59983488	0.84[ASN][1000 genomes]
rs60346641	0.85[ASN][1000 genomes]
rs60826731	0.85[ASN][1000 genomes]
rs6458419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs6458420	0.81[ASN][1000 genomes]
rs6458423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6458425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6458427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6458428	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458430	0.86[ASN][1000 genomes]
rs6458435	0.89[JPT][hapmap]
rs6458440	0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6458441	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6899378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6899763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6901786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6905396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6917352	0.89[JPT][hapmap]
rs6919847	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6922660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6922772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6926638	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6928753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6932804	0.97[ASN][1000 genomes]
rs6932926	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6933449	0.97[ASN][1000 genomes]
rs6934594	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935398	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6936475	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs6937317	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6938316	0.85[ASN][1000 genomes]
rs6941169	0.82[ASN][1000 genomes]
rs73735354	0.85[ASN][1000 genomes]
rs73735357	0.85[ASN][1000 genomes]
rs73735369	0.85[ASN][1000 genomes]
rs73735378	0.85[ASN][1000 genomes]
rs7451423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7738526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7739928	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7740083	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7740542	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs7743116	0.81[AMR][1000 genomes]
rs7750380	0.82[ASN][1000 genomes]
rs7757282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7760112	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7767025	0.92[ASN][1000 genomes]
rs7769231	0.98[ASN][1000 genomes]
rs7770401	0.86[EUR][1000 genomes]
rs927658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9296453	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9296457	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296458	0.98[ASN][1000 genomes]
rs9349313	0.81[ASN][1000 genomes]
rs9349315	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357470	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9357471	0.86[CEU][hapmap]
rs9357478	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357480	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369534	0.82[ASN][1000 genomes]
rs9369549	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs9369552	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9369558	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];0.98[ASN][1000 genomes]
rs9381364	0.82[ASN][1000 genomes]
rs9381365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9381366	0.81[ASN][1000 genomes]
rs9381373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9381377	0.82[EUR][1000 genomes]
rs9381383	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9395066	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs9395079	0.83[AMR][1000 genomes]
rs9395081	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs9395084	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9395086	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9395087	0.86[EUR][1000 genomes]
rs9395088	0.90[ASN][1000 genomes]
rs9395095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9463076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9463078	0.84[CEU][hapmap]
rs9463081	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463083	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472442	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs9472451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9472453	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs9472460	0.81[EUR][1000 genomes]
rs964452	0.85[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs967588	0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs988147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2763550	chr6:45186825-45275593	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830652	chr6:45187467-45328983	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4446571	SUPT3H	cis	multi-tissue	Pritchard
rs4446571	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45249800-45278200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:45254800-45258800	Weak transcription	Dnd41	blood
3	chr6:45257400-45259400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:45257600-45257800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:45257600-45257800	Enhancers	Aorta	Aorta
6	chr6:45257600-45259400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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