Variant report

Variant	rs1864617
Chromosome Location	chr3:87948318-87948319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11926472	0.88[EUR][1000 genomes]
rs12492995	0.88[EUR][1000 genomes]
rs13324246	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1393915	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1465648	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1503425	0.83[AFR][1000 genomes]
rs1503426	0.83[AFR][1000 genomes]
rs1503428	0.87[AFR][1000 genomes]
rs1503430	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1604701	0.83[AFR][1000 genomes]
rs17025160	0.82[ASN][1000 genomes]
rs17025198	0.88[EUR][1000 genomes]
rs17025201	0.87[EUR][1000 genomes]
rs1811618	0.82[ASN][1000 genomes]
rs2062811	0.83[AFR][1000 genomes]
rs2116145	0.88[EUR][1000 genomes]
rs2163420	0.82[ASN][1000 genomes]
rs28854202	0.82[ASN][1000 genomes]
rs2915288	0.87[AFR][1000 genomes]
rs2919267	0.87[AFR][1000 genomes]
rs2919272	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932274	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2932277	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932301	0.84[AFR][1000 genomes]
rs2938265	0.83[AFR][1000 genomes]
rs2938268	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2938270	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55649543	0.82[ASN][1000 genomes]
rs6551260	0.88[EUR][1000 genomes]
rs6770080	0.82[ASN][1000 genomes]
rs6782603	0.82[ASN][1000 genomes]
rs6790293	0.82[ASN][1000 genomes]
rs6807663	0.82[ASN][1000 genomes]
rs6809560	0.82[ASN][1000 genomes]
rs72913785	0.82[ASN][1000 genomes]
rs72915609	0.82[ASN][1000 genomes]
rs73847728	0.82[ASN][1000 genomes]
rs73847730	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7631129	0.82[ASN][1000 genomes]
rs7646120	0.82[ASN][1000 genomes]
rs7646993	0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs7649800	0.82[ASN][1000 genomes]
rs9310058	0.88[EUR][1000 genomes]
rs9812937	0.82[ASN][1000 genomes]
rs9836185	0.87[EUR][1000 genomes]
rs9838596	0.82[ASN][1000 genomes]
rs9850490	0.87[EUR][1000 genomes]
rs9853753	0.82[ASN][1000 genomes]
rs9869636	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs989563	0.83[AFR][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	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	nsv460757	chr3:87863280-87949733	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	nsv590919	chr3:87863280-87949733	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
5	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
6	esv2760794	chr3:87932310-87953742	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv1001572	chr3:87942288-87983962	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1864617	CGGBP1	cis	parietal	SCAN
rs1864617	HTR1F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87944400-87948600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:87947600-87949200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:87947800-87951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:87948000-87948400	Enhancers	Pancreatic Islets	Pancreatic Islet

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