Variant report

Variant	rs1161603
Chromosome Location	chr9:27098940-27098941
allele	C/T
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	STAT3	chr9:27098794-27098952	MCF10A-Er-Src	breast:	n/a	chr9:27098840-27098852

Variant related genes	Relation type
ENSG00000254396	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10511793	1.00[CHB][hapmap]
rs10812492	1.00[CHB][hapmap]
rs10812500	1.00[CHB][hapmap]
rs10967593	1.00[CHB][hapmap]
rs10967594	1.00[CHB][hapmap]
rs10967624	1.00[CHB][hapmap]
rs10967625	1.00[CHB][hapmap]
rs10967634	1.00[CHB][hapmap]
rs10967639	1.00[CHB][hapmap]
rs10967640	1.00[CHB][hapmap]
rs11788136	1.00[CHB][hapmap]
rs12001845	1.00[CHB][hapmap]
rs12005388	1.00[CHB][hapmap]
rs12337860	1.00[CHB][hapmap]
rs12338678	1.00[CHB][hapmap]
rs12339162	1.00[CHB][hapmap]
rs12340500	1.00[CHB][hapmap]
rs12343345	1.00[CHB][hapmap]
rs12345094	1.00[CHB][hapmap]
rs12349359	1.00[CHB][hapmap]
rs12352441	1.00[CHB][hapmap]
rs12352603	1.00[CHB][hapmap]
rs12352631	1.00[CHB][hapmap]
rs12554485	1.00[CHB][hapmap]
rs13293051	1.00[CHB][hapmap]
rs1591356	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910888	1.00[CHB][hapmap]
rs16910895	1.00[CHB][hapmap]
rs16911083	1.00[CHB][hapmap]
rs17694300	1.00[CHB][hapmap]
rs17694306	1.00[CHB][hapmap]
rs17694549	1.00[CHB][hapmap]
rs17694796	1.00[CHB][hapmap]
rs17756599	1.00[CHB][hapmap]
rs17756667	1.00[CHB][hapmap]
rs17756685	1.00[CHB][hapmap]
rs2027124	1.00[CHB][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3429	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs610195	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs615532	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs62542704	0.81[ASN][1000 genomes]
rs62542705	0.81[ASN][1000 genomes]
rs62542706	0.81[ASN][1000 genomes]
rs62542707	0.81[ASN][1000 genomes]
rs625630	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627339	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639826	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475948	1.00[CHB][hapmap]
rs6475959	1.00[CHB][hapmap]
rs6475963	1.00[CHB][hapmap]
rs6475966	1.00[CHB][hapmap]
rs6475968	1.00[CHB][hapmap]
rs7037860	1.00[CHB][hapmap]
rs7039400	1.00[CHB][hapmap]
rs7040772	1.00[CHB][hapmap]
rs7042003	1.00[CHB][hapmap]
rs7042119	1.00[CHB][hapmap]
rs7044842	1.00[CHB][hapmap]
rs73438223	0.81[ASN][1000 genomes]
rs7847280	1.00[CHB][hapmap]
rs7854048	1.00[CHB][hapmap]
rs7871097	1.00[CHB][hapmap]
rs7871178	1.00[CHB][hapmap]
rs7871286	1.00[CHB][hapmap]
rs7873019	1.00[CHB][hapmap]
rs7873161	1.00[CHB][hapmap]
rs7873329	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv466334	chr9:27028947-27098940	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv613944	chr9:27028947-27098940	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1161603	IFT74	cis	lymphoblastoid	seeQTL
rs1161603	C9orf82	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27095200-27108800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:27095600-27102200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:27095600-27108800	Weak transcription	NH-A	brain
4	chr9:27096800-27109000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:27098400-27108800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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