Variant report

Variant	rs3852401
Chromosome Location	chr9:97333275-97333276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97332451..97335013-chr9:97342428..97345241,2	MCF-7	breast:
2	chr9:97322900..97325527-chr9:97331742..97334023,2	MCF-7	breast:
3	chr9:97219790..97221474-chr9:97332008..97334715,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10115132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120467	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048510	0.85[YRI][hapmap]
rs10761339	0.85[YRI][hapmap]
rs1754432	0.92[LWK][hapmap];0.85[MKK][hapmap];0.83[YRI][hapmap]
rs2406664	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2406665	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2406666	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2772011	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2772012	0.87[AFR][1000 genomes]
rs2945795	0.85[AFR][1000 genomes]
rs2945796	0.96[YRI][hapmap]
rs2945798	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2987883	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2993963	0.87[AFR][1000 genomes]
rs35600708	0.80[EUR][1000 genomes]
rs4744354	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478604	0.87[AFR][1000 genomes]
rs498533	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs498635	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs501380	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs509022	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs540236	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs55869080	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558753	0.87[AFR][1000 genomes]
rs55983816	0.91[EUR][1000 genomes]
rs56404355	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564430	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs586140	0.87[LWK][hapmap];0.85[MKK][hapmap];0.83[YRI][hapmap]
rs597003	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs598386	0.97[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs599229	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs609901	0.97[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs612115	0.84[AFR][1000 genomes]
rs612202	0.85[AFR][1000 genomes]
rs612498	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs612952	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs642035	0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs642477	0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs642952	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs644237	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs645125	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs660911	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs693122	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7025414	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73653487	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7851565	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv521698	chr9:97333275-97338221	Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3852401	FBP1	cis	multi-tissue	Pritchard
rs3852401	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs3852401	IARS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97317200-97354000	Weak transcription	Gastric	stomach
2	chr9:97325800-97339200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:97326800-97339200	Weak transcription	Fetal Stomach	stomach
4	chr9:97331400-97340000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:97333200-97335400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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