Variant report

Variant	rs9369523
Chromosome Location	chr6:44908728-44908729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1041333	0.90[EUR][1000 genomes]
rs10948186	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs10948187	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs10948190	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs10948194	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs10948195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12191518	0.90[EUR][1000 genomes]
rs12216059	1.00[YRI][hapmap]
rs1293598	0.90[EUR][1000 genomes]
rs1329716	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs1360196	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1555681	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1576382	0.91[EUR][1000 genomes]
rs1854547	0.90[EUR][1000 genomes]
rs1935551	0.88[EUR][1000 genomes]
rs1980265	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2145826	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2396370	0.91[EUR][1000 genomes]
rs2396371	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2396373	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778507	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs3799967	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs3799968	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs3799971	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs3799978	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3846896	0.90[EUR][1000 genomes]
rs494982	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs57020561	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs636845	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs6458415	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs6903576	0.90[EUR][1000 genomes]
rs6904015	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs6910294	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs6910749	0.80[EUR][1000 genomes]
rs6919485	0.89[EUR][1000 genomes]
rs6923519	0.91[EUR][1000 genomes]
rs6940547	0.82[EUR][1000 genomes]
rs7754698	0.87[EUR][1000 genomes]
rs929614	0.80[EUR][1000 genomes]
rs9296448	0.81[EUR][1000 genomes]
rs9349303	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9357459	0.88[EUR][1000 genomes]
rs9357464	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs9357469	0.82[CEU][hapmap]
rs9357471	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9367208	0.89[EUR][1000 genomes]
rs9367211	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs9369512	0.85[EUR][1000 genomes]
rs9369513	0.88[EUR][1000 genomes]
rs9369514	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs9369515	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9369516	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs9381359	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9395049	0.82[CEU][hapmap]
rs9395051	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs9395055	0.92[EUR][1000 genomes]
rs9463054	0.91[EUR][1000 genomes]
rs9463055	0.90[EUR][1000 genomes]
rs9472383	0.87[EUR][1000 genomes]
rs9472403	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472418	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs976699	0.84[CEU][hapmap];0.90[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	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	nsv1033815	chr6:44845514-44938799	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv5286	chr6:44865290-44909915	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9369523	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs9369523	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44895800-44910200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:44904400-44918800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:44905200-44913200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:44906800-44913400	Weak transcription	HSMM	muscle
5	chr6:44907600-44909200	Enhancers	HepG2	liver
6	chr6:44908000-44910400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:44908200-44908800	Enhancers	Liver	Liver
8	chr6:44908600-44909000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr6:44908600-44910000	ZNF genes & repeats	Dnd41	blood

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