Variant report

Variant	rs3904534
Chromosome Location	chr9:93532294-93532295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93531677..93533419-chr9:93534345..93537037,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10821495	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821496	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821506	1.00[ASN][1000 genomes]
rs10821507	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10993655	0.81[EUR][1000 genomes]
rs10993670	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10993691	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11496668	0.81[EUR][1000 genomes]
rs11521686	0.84[EUR][1000 genomes]
rs1172991	0.83[AFR][1000 genomes]
rs12377987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551476	0.81[EUR][1000 genomes]
rs12553630	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283061	0.84[EUR][1000 genomes]
rs13288981	0.85[EUR][1000 genomes]
rs34221447	1.00[ASN][1000 genomes]
rs34518167	0.84[EUR][1000 genomes]
rs35649391	0.84[EUR][1000 genomes]
rs35997145	0.85[EUR][1000 genomes]
rs7470845	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv482757	chr9:93356095-93543903	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv968728	chr9:93494212-93532434	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3904534	SYK	Cis_1M	lymphoblastoid	RTeQTL
rs3904534	SYK	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93529600-93536200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:93530600-93538400	Enhancers	Primary B cells from peripheral blood	blood
3	chr9:93530800-93538200	Enhancers	Primary B cells from cord blood	blood
4	chr9:93531000-93534400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr9:93531600-93533800	Enhancers	GM12878-XiMat	blood
6	chr9:93531600-93537600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr9:93531800-93533200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:93532000-93532600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:93532000-93532600	Enhancers	Spleen	Spleen
10	chr9:93532000-93533600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:93532200-93532800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:93532200-93533600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:93532200-93537400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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