Variant report

Variant	rs12208339
Chromosome Location	chr6:44993512-44993513
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	chr6:44987589..44991130-chr6:44992558..44996333,3	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1023089	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1023090	0.85[ASN][1000 genomes]
rs1041332	0.86[ASN][1000 genomes]
rs10456119	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10484627	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10948183	0.81[ASN][1000 genomes]
rs10948185	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10948186	0.84[ASN][1000 genomes]
rs10948192	0.88[EUR][1000 genomes]
rs10948193	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10948197	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10948198	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150806	0.82[ASN][1000 genomes]
rs11967188	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11968042	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12190261	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12191518	0.83[ASN][1000 genomes]
rs12198904	0.81[ASN][1000 genomes]
rs12205071	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208023	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208483	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12209076	0.82[ASN][1000 genomes]
rs12214778	0.80[EUR][1000 genomes]
rs12524069	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12525009	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12526711	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12528762	0.84[ASN][1000 genomes]
rs12529490	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1284972	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1284973	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1284975	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1284980	0.81[EUR][1000 genomes]
rs1284982	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1284983	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1284988	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1284992	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1285026	0.81[EUR][1000 genomes]
rs1300126	0.81[EUR][1000 genomes]
rs13201942	0.84[ASN][1000 genomes]
rs13202529	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13205113	0.84[ASN][1000 genomes]
rs13207575	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13209827	0.82[ASN][1000 genomes]
rs13211229	0.80[EUR][1000 genomes]
rs1324532	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1329710	0.81[ASN][1000 genomes]
rs1329713	0.89[ASN][1000 genomes]
rs1329714	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1578676	0.84[ASN][1000 genomes]
rs1590864	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17424547	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1831310	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1937046	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1937047	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1971482	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2186062	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2396372	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2396375	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34808716	0.80[ASN][1000 genomes]
rs35357222	0.88[EUR][1000 genomes]
rs35813980	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3778507	0.83[ASN][1000 genomes]
rs3799976	0.83[ASN][1000 genomes]
rs3799977	0.82[ASN][1000 genomes]
rs3799981	0.81[ASN][1000 genomes]
rs3799984	0.81[ASN][1000 genomes]
rs3799986	0.84[ASN][1000 genomes]
rs3846896	0.81[ASN][1000 genomes]
rs4398713	0.90[ASN][1000 genomes]
rs4412189	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711803	0.81[ASN][1000 genomes]
rs4711805	0.81[ASN][1000 genomes]
rs4711807	0.83[EUR][1000 genomes]
rs4714830	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4714832	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4714836	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs500773	0.81[ASN][1000 genomes]
rs55893720	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs608941	0.81[ASN][1000 genomes]
rs6458414	0.80[ASN][1000 genomes]
rs6458418	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs679713	0.84[ASN][1000 genomes]
rs6923436	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6925467	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6933553	0.83[ASN][1000 genomes]
rs7742360	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7749865	0.84[EUR][1000 genomes]
rs7758031	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7763421	0.81[ASN][1000 genomes]
rs7763450	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7764102	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7775717	0.81[ASN][1000 genomes]
rs9349309	0.83[ASN][1000 genomes]
rs9367214	0.83[ASN][1000 genomes]
rs9369516	0.81[ASN][1000 genomes]
rs9369529	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9369530	0.83[ASN][1000 genomes]
rs9381361	0.86[ASN][1000 genomes]
rs9395065	0.83[EUR][1000 genomes]
rs9472407	0.84[ASN][1000 genomes]
rs969211	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	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
10	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	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
14	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
15	nsv603008	chr6:44958372-45081821	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2762589	chr6:44982992-45044580	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12208339	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44966400-44993600	Weak transcription	HepG2	liver
2	chr6:44974800-45004600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:44977600-44993800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:44981600-44994800	Weak transcription	Aorta	Aorta
5	chr6:44981600-44994800	Weak transcription	Pancreas	Pancrea

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