Variant report

Variant	rs12204678
Chromosome Location	chr6:45121699-45121700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45120420..45122464-chr6:45122631..45125594,2	K562	blood:
2	chr6:45119653..45122627-chr6:45134013..45136661,2	MCF-7	breast:

Extended variants
information (count: 172 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1023090	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1041332	0.80[ASN][1000 genomes]
rs1080415	0.87[ASN][1000 genomes]
rs10807318	0.90[ASN][1000 genomes]
rs10807319	0.87[ASN][1000 genomes]
rs10807320	0.86[ASN][1000 genomes]
rs10948222	0.83[ASN][1000 genomes]
rs11968042	0.87[ASN][1000 genomes]
rs12190261	0.81[ASN][1000 genomes]
rs12205071	0.82[ASN][1000 genomes]
rs12205274	0.83[ASN][1000 genomes]
rs12208023	0.82[ASN][1000 genomes]
rs12208483	0.87[ASN][1000 genomes]
rs12529946	0.83[ASN][1000 genomes]
rs12530207	0.82[ASN][1000 genomes]
rs12662272	0.84[ASN][1000 genomes]
rs1284955	0.80[ASN][1000 genomes]
rs1284961	0.92[ASN][1000 genomes]
rs1284965	0.90[ASN][1000 genomes]
rs1284969	0.87[ASN][1000 genomes]
rs1284972	0.94[ASN][1000 genomes]
rs1284973	0.96[ASN][1000 genomes]
rs1284975	0.96[ASN][1000 genomes]
rs1284979	0.83[ASN][1000 genomes]
rs1284980	0.85[ASN][1000 genomes]
rs1284988	0.93[ASN][1000 genomes]
rs1284992	0.93[ASN][1000 genomes]
rs1284993	0.81[ASN][1000 genomes]
rs1284995	0.82[ASN][1000 genomes]
rs1284999	0.83[ASN][1000 genomes]
rs1285003	0.83[ASN][1000 genomes]
rs1285004	0.96[ASN][1000 genomes]
rs1285005	0.84[ASN][1000 genomes]
rs1285006	0.84[ASN][1000 genomes]
rs1285007	0.85[ASN][1000 genomes]
rs1285008	0.84[ASN][1000 genomes]
rs1285009	0.84[ASN][1000 genomes]
rs1285010	0.84[ASN][1000 genomes]
rs1285011	0.84[ASN][1000 genomes]
rs1285013	0.89[ASN][1000 genomes]
rs1285014	0.89[ASN][1000 genomes]
rs1285019	0.92[ASN][1000 genomes]
rs1285020	0.85[ASN][1000 genomes]
rs1285021	0.84[ASN][1000 genomes]
rs1285022	0.98[ASN][1000 genomes]
rs1285023	0.98[ASN][1000 genomes]
rs1285025	0.83[ASN][1000 genomes]
rs1285026	0.98[ASN][1000 genomes]
rs1285027	0.85[ASN][1000 genomes]
rs1285028	0.84[ASN][1000 genomes]
rs1285029	0.84[ASN][1000 genomes]
rs1285030	0.84[ASN][1000 genomes]
rs1285031	0.83[ASN][1000 genomes]
rs1290386	0.92[ASN][1000 genomes]
rs1300126	0.96[ASN][1000 genomes]
rs1304168	0.89[ASN][1000 genomes]
rs13207575	0.82[ASN][1000 genomes]
rs1324531	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1324532	0.93[ASN][1000 genomes]
rs1324535	0.84[ASN][1000 genomes]
rs1324537	0.98[ASN][1000 genomes]
rs1324540	0.86[ASN][1000 genomes]
rs1329713	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1359336	0.94[ASN][1000 genomes]
rs1411148	0.88[ASN][1000 genomes]
rs1555681	0.86[EUR][1000 genomes]
rs1581777	0.87[ASN][1000 genomes]
rs1629542	0.87[ASN][1000 genomes]
rs1748231	0.87[ASN][1000 genomes]
rs1748234	0.87[ASN][1000 genomes]
rs1748235	0.87[ASN][1000 genomes]
rs1748237	0.84[ASN][1000 genomes]
rs1748242	0.87[ASN][1000 genomes]
rs1797145	0.87[ASN][1000 genomes]
rs1797147	0.86[ASN][1000 genomes]
rs1797148	0.81[ASN][1000 genomes]
rs1797149	0.81[ASN][1000 genomes]
rs1797156	0.81[ASN][1000 genomes]
rs1886345	0.97[ASN][1000 genomes]
rs1937046	0.84[ASN][1000 genomes]
rs1937047	0.87[ASN][1000 genomes]
rs2038766	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2093901	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093903	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2186062	0.80[ASN][1000 genomes]
rs2396380	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2396381	0.81[ASN][1000 genomes]
rs2396425	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35817842	0.80[ASN][1000 genomes]
rs3920903	0.88[ASN][1000 genomes]
rs4352679	0.86[ASN][1000 genomes]
rs4412189	0.80[ASN][1000 genomes]
rs4714836	0.82[ASN][1000 genomes]
rs4714845	0.87[ASN][1000 genomes]
rs4714847	0.87[ASN][1000 genomes]
rs4714848	0.87[ASN][1000 genomes]
rs56138724	0.88[ASN][1000 genomes]
rs6458419	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458420	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458423	0.86[ASN][1000 genomes]
rs6458425	0.92[ASN][1000 genomes]
rs6458427	0.90[ASN][1000 genomes]
rs6458428	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6458430	0.90[ASN][1000 genomes]
rs6899378	0.96[ASN][1000 genomes]
rs6899845	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6901786	0.90[ASN][1000 genomes]
rs6905396	0.92[ASN][1000 genomes]
rs6917594	0.84[ASN][1000 genomes]
rs6923436	0.87[ASN][1000 genomes]
rs6933553	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6937317	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6938316	0.90[ASN][1000 genomes]
rs6941169	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73449282	0.84[ASN][1000 genomes]
rs7451423	0.83[ASN][1000 genomes]
rs7738526	0.92[ASN][1000 genomes]
rs7739928	0.91[ASN][1000 genomes]
rs7743116	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750380	0.94[ASN][1000 genomes]
rs7758031	0.82[ASN][1000 genomes]
rs7763450	0.86[ASN][1000 genomes]
rs7763973	0.80[ASN][1000 genomes]
rs7767025	0.81[ASN][1000 genomes]
rs927658	0.92[ASN][1000 genomes]
rs9296453	0.87[ASN][1000 genomes]
rs9296455	0.86[ASN][1000 genomes]
rs9349309	0.83[ASN][1000 genomes]
rs9349313	0.98[ASN][1000 genomes]
rs9349315	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357469	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357470	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357471	0.84[EUR][1000 genomes]
rs9357478	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357480	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9367214	0.83[ASN][1000 genomes]
rs9369530	0.82[ASN][1000 genomes]
rs9369533	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9369534	0.94[ASN][1000 genomes]
rs9369552	0.80[EUR][1000 genomes]
rs9381361	0.80[ASN][1000 genomes]
rs9381364	0.94[ASN][1000 genomes]
rs9381365	0.97[ASN][1000 genomes]
rs9381366	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9381373	0.90[ASN][1000 genomes]
rs9381377	0.80[EUR][1000 genomes]
rs9395063	0.88[ASN][1000 genomes]
rs9395065	0.93[ASN][1000 genomes]
rs9395066	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9395069	0.89[EUR][1000 genomes]
rs9395079	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9395086	0.87[ASN][1000 genomes]
rs9395088	0.86[ASN][1000 genomes]
rs9463069	0.80[ASN][1000 genomes]
rs9463076	0.90[ASN][1000 genomes]
rs9463078	0.82[EUR][1000 genomes]
rs9463081	0.87[ASN][1000 genomes]
rs9472442	0.84[ASN][1000 genomes]
rs9472451	0.87[ASN][1000 genomes]
rs964452	0.91[ASN][1000 genomes]
rs969211	0.82[ASN][1000 genomes]
rs988147	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1026728	chr6:45001948-45126730	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538213	chr6:45001948-45126730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1032906	chr6:45069368-45212863	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12204678	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45119800-45121800	Weak transcription	Dnd41	blood
2	chr6:45121200-45122200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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