Variant report

Variant	rs1489777
Chromosome Location	chr3:87863280-87863281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:87861321..87864231-chr3:87868355..87870648,2	K562	blood:
2	chr3:87859784..87864231-chr3:87868098..87870648,4	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1156395	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12485486	0.85[ASN][1000 genomes]
rs12490277	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12633947	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13316021	0.81[ASN][1000 genomes]
rs1489778	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1602152	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602154	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025015	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847309	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2010539	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029437	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2130351	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171821	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28872274	0.81[ASN][1000 genomes]
rs2919238	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919240	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919242	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919248	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932270	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932281	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2932282	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932296	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932298	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932309	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932310	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859104	0.87[CHD][hapmap]
rs55788242	0.82[ASN][1000 genomes]
rs57844811	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67303034	0.80[ASN][1000 genomes]
rs6779623	0.82[ASN][1000 genomes]
rs7619960	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs923475	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs923477	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9867061	0.87[CHB][hapmap];0.81[CHD][hapmap];0.81[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	nsv590918	chr3:87323334-87910931	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv834756	chr3:87763793-87938179	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1489777	HTR1F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87860600-87863400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:87860600-87863800	Weak transcription	HUVEC	blood vessel
3	chr3:87861400-87864600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:87862600-87864000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:87862600-87866600	Weak transcription	K562	blood
6	chr3:87862800-87874800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:87863200-87863400	Strong transcription	Primary hematopoietic stem cells	blood

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