Variant report

Variant	rs9869636
Chromosome Location	chr3:87994962-87994963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11926472	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12492995	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13324246	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393915	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465648	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1503430	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17025160	0.86[ASN][1000 genomes]
rs17025198	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17025201	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1811618	0.86[ASN][1000 genomes]
rs1864617	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2116145	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2163420	0.86[ASN][1000 genomes]
rs28854202	0.86[ASN][1000 genomes]
rs2919272	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932274	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2932277	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2938268	0.81[ASN][1000 genomes]
rs2938270	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55649543	0.86[ASN][1000 genomes]
rs6551260	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6770080	0.86[ASN][1000 genomes]
rs6782603	0.86[ASN][1000 genomes]
rs6790293	0.86[ASN][1000 genomes]
rs6807663	0.86[ASN][1000 genomes]
rs6809560	0.86[ASN][1000 genomes]
rs72913785	0.86[ASN][1000 genomes]
rs72915609	0.86[ASN][1000 genomes]
rs73847728	0.86[ASN][1000 genomes]
rs73847730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631129	0.86[ASN][1000 genomes]
rs7646120	0.86[ASN][1000 genomes]
rs7646993	1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs7649800	0.86[ASN][1000 genomes]
rs9310058	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9812937	0.86[ASN][1000 genomes]
rs9836185	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9838596	0.86[ASN][1000 genomes]
rs9839638	0.89[ASN][1000 genomes]
rs9850490	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9853753	0.86[ASN][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	nsv1009981	chr3:87821573-88003956	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv536634	chr3:87821573-88003956	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv834758	chr3:87867363-88014975	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1007981	chr3:87949316-88004036	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv527929	chr3:87949733-88003812	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9869636	HTR1F	cis	parietal	SCAN
rs9869636	CGGBP1	cis	parietal	SCAN
rs9869636	NT5C2	trans	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87994400-87995000	Strong transcription	Primary hematopoietic stem cells	blood
2	chr3:87994400-87995600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:87994800-87995400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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