Variant report

Variant	rs17420300
Chromosome Location	chr1:80054293-80054294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10874047	0.88[ASN][1000 genomes]
rs12088600	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730647	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1339784	0.92[ASN][1000 genomes]
rs1339787	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1382968	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1382969	0.90[ASN][1000 genomes]
rs1389942	0.96[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs1479738	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1479740	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556942	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17420481	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17454224	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000101	0.86[CEU][hapmap]
rs34420593	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34763301	0.81[ASN][1000 genomes]
rs34898118	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506421	0.87[CEU][hapmap]
rs4650322	0.86[EUR][1000 genomes]
rs6665873	0.92[ASN][1000 genomes]
rs7551776	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987961	0.92[ASN][1000 genomes]
rs9943179	0.88[AMR][1000 genomes];0.95[ASN][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	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv546636	chr1:79964823-80079996	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546637	chr1:79984748-80159969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3393619	chr1:80018980-80054975	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17420300	IFI44	cis	lymphoblastoid	seeQTL
rs17420300	HERC5	trans	lymphoblastoid	seeQTL
rs17420300	IFI44L	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:80052800-80058800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr1:80053000-80055600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr1:80053600-80054400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:80053800-80054800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:80053800-80056000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:80053800-80057600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:80053800-80058000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:80054200-80054400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr1:80054200-80054400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:80054200-80054600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:80054200-80054800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:80054200-80055000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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