Variant report

Variant	rs41439648
Chromosome Location	chr9:15885637-15885638
allele	A/C
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	POLR2A	chr9:15885447-15885909	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr9:15885600-15885750	HCFaa	heart:	n/a	n/a

Variant related genes	Relation type
CCDC171	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11998843	1.00[AMR][1000 genomes]
rs12001109	1.00[AMR][1000 genomes]
rs12002511	1.00[AMR][1000 genomes]
rs12003371	1.00[AMR][1000 genomes]
rs1328270	1.00[AMR][1000 genomes]
rs1328272	1.00[AMR][1000 genomes]
rs16933587	1.00[ASW][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16933906	1.00[AMR][1000 genomes]
rs1857024	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2149232	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs56312242	1.00[AMR][1000 genomes]
rs56679179	1.00[AMR][1000 genomes]
rs56754898	1.00[AMR][1000 genomes]
rs56774729	1.00[AMR][1000 genomes]
rs56818091	1.00[AMR][1000 genomes]
rs57158144	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57351686	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57779097	1.00[AMR][1000 genomes]
rs58010776	1.00[AMR][1000 genomes]
rs58373606	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58603418	1.00[AMR][1000 genomes]
rs58970083	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58999162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59106947	1.00[AMR][1000 genomes]
rs59198717	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59352577	1.00[AMR][1000 genomes]
rs59574569	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59655011	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59703985	1.00[AMR][1000 genomes]
rs59860684	1.00[AMR][1000 genomes]
rs59882619	1.00[AMR][1000 genomes]
rs60249192	1.00[AMR][1000 genomes]
rs60322090	1.00[AMR][1000 genomes]
rs60418791	1.00[AMR][1000 genomes]
rs60581753	1.00[AMR][1000 genomes]
rs60641653	1.00[AMR][1000 genomes]
rs60655538	1.00[AMR][1000 genomes]
rs60692567	1.00[AMR][1000 genomes]
rs60846086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60911267	1.00[AMR][1000 genomes]
rs60997329	1.00[AMR][1000 genomes]
rs61481057	1.00[AMR][1000 genomes]
rs73411539	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411548	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411550	1.00[AMR][1000 genomes]
rs73411556	1.00[AMR][1000 genomes]
rs73411562	1.00[AMR][1000 genomes]
rs73411564	1.00[AMR][1000 genomes]
rs73411587	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413909	1.00[AMR][1000 genomes]
rs73413926	1.00[AMR][1000 genomes]
rs73413946	1.00[AMR][1000 genomes]
rs73413991	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417830	1.00[AMR][1000 genomes]
rs73418180	1.00[AMR][1000 genomes]
rs73420322	1.00[AMR][1000 genomes]
rs73420371	1.00[AMR][1000 genomes]
rs73420377	1.00[AMR][1000 genomes]
rs73420384	1.00[AMR][1000 genomes]
rs73420388	1.00[AMR][1000 genomes]
rs73422705	1.00[AMR][1000 genomes]
rs73422726	1.00[AMR][1000 genomes]
rs73422740	1.00[AMR][1000 genomes]
rs73422753	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73424824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73424825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73424832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73424853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73644942	1.00[AMR][1000 genomes]
rs73644943	1.00[AMR][1000 genomes]
rs73644945	1.00[AMR][1000 genomes]
rs73644946	1.00[AMR][1000 genomes]
rs73644957	1.00[AMR][1000 genomes]
rs73644958	1.00[AMR][1000 genomes]
rs73644961	1.00[AMR][1000 genomes]
rs73645248	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv892633	chr9:15604746-15889411	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15877000-15903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:15877400-15885800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:15877600-15888400	Weak transcription	Pancreas	Pancrea
4	chr9:15884200-15891800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:15884200-15892200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:15885400-15885800	Strong transcription	Primary hematopoietic stem cells	blood
7	chr9:15885400-15886800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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