Variant report

Variant	rs325639
Chromosome Location	chr11:6149225-6149226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr11:6148956-6149585	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr11:6149113-6149486	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr11:6149187-6149456	HUVEC	blood vessel:	n/a	n/a
4	FOS	chr11:6149138-6149344	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr11:6149122-6149455	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA2	chr11:6148552-6149769	HUVEC	blood vessel:	n/a	chr11:6149279-6149286 chr11:6149653-6149663 chr11:6149652-6149668 chr11:6149274-6149288 chr11:6149656-6149663 chr11:6149279-6149286 chr11:6149656-6149663 chr11:6149655-6149665 chr11:6149654-6149666 chr11:6149275-6149291 chr11:6149272-6149293 chr11:6149279-6149286 chr11:6149656-6149663
7	FOS	chr11:6149104-6149486	MCF10A-Er-Src	breast:	n/a	n/a
8	JUN	chr11:6149120-6149520	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
OR56B3P	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10839517	0.81[ASN][1000 genomes]
rs10839519	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11040772	0.81[ASN][1000 genomes]
rs11826453	0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs1381911	0.82[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1599692	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1903778	0.94[ASN][1000 genomes]
rs2221718	0.81[ASN][1000 genomes]
rs325634	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs325636	0.83[EUR][1000 genomes]
rs325640	0.82[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs325657	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs325661	0.92[ASN][1000 genomes]
rs325666	0.97[ASN][1000 genomes]
rs325697	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs34220108	0.81[ASN][1000 genomes]
rs3921908	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4520575	0.94[ASN][1000 genomes]
rs4758078	0.94[ASN][1000 genomes]
rs4758085	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758086	0.83[ASN][1000 genomes]
rs4758380	0.94[ASN][1000 genomes]
rs4758392	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6578740	0.94[ASN][1000 genomes]
rs6578742	0.83[EUR][1000 genomes]
rs6578743	0.86[ASN][1000 genomes]
rs6578744	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7117911	0.94[ASN][1000 genomes]
rs7480133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930953	0.83[ASN][1000 genomes]
rs7944650	0.94[ASN][1000 genomes]
rs7948429	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv522884	chr11:6144998-6164700	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv467697	chr11:6144998-6164700	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
7	nsv553370	chr11:6144998-6164700	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs325639	OR51A4	cis	cerebellum	SCAN
rs325639	OR52N2	cis	parietal	SCAN
rs325639	FAM160A2	cis	parietal	SCAN
rs325639	TMEM9B	cis	parietal	SCAN
rs325639	DNHD1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:6147800-6150200	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr11:6148400-6150000	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr11:6148600-6153000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:6148800-6150000	Enhancers	HUVEC	blood vessel

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