Variant report

Variant	rs12488028
Chromosome Location	chr3:87850799-87850800
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	chr3:87849890..87852917-chr3:87853922..87857395,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12485486	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489435	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633947	0.81[ASN][1000 genomes]
rs1489778	0.81[ASN][1000 genomes]
rs1489780	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1873209	0.83[ASN][1000 genomes]
rs1873210	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2046796	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130351	0.81[ASN][1000 genomes]
rs2880695	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4630962	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859104	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55754932	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55788242	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55807523	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56125632	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56169023	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56386821	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57844811	0.81[ASN][1000 genomes]
rs67303034	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779623	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643136	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	nsv877142	chr3:87630433-87854277	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv877143	chr3:87630433-87860130	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12488028	HTR1F	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87842600-87851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:87845600-87855800	Weak transcription	A549	lung
3	chr3:87848600-87850800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:87849400-87852400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:87849600-87851000	Enhancers	K562	blood
6	chr3:87849800-87851000	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:87850200-87850800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:87850400-87850800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:87850400-87850800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:87850400-87851000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:87850600-87850800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:87850600-87851000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:87850600-87851000	Enhancers	Fetal Thymus	thymus

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