Variant report

Variant	rs4294380
Chromosome Location	chr1:227578985-227578986
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:227578964-227579934	K562	blood:	n/a	chr1:227579355-227579365 chr1:227579210-227579221 chr1:227579209-227579221 chr1:227579351-227579365
2	EP300	chr1:227578962-227579286	K562	blood:	n/a	chr1:227579175-227579189
3	TAL1	chr1:227578890-227579728	K562	blood:	n/a	chr1:227579648-227579663 chr1:227579648-227579663
4	TEAD4	chr1:227578851-227579313	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227571064..227573731-chr1:227576729..227579706,2	MCF-7	breast:
2	chr1:227573402..227580584-chr1:227581981..227587587,10	K562	blood:
3	chr1:227508074..227511114-chr1:227576547..227579179,3	K562	blood:
4	chr1:227578119..227581046-chr11:66042464..66044320,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234277	TF binding region

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

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

rs_ID	r²[population]
rs10753434	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799412	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10916129	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs10916133	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12022338	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12023427	0.81[YRI][hapmap]
rs12028523	0.81[YRI][hapmap]
rs12045794	0.86[AFR][1000 genomes]
rs12057466	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs16847690	0.80[CHB][hapmap]
rs3000777	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3014272	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3014274	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4075196	0.80[CHB][hapmap]
rs4233227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489522	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4491034	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653498	0.80[CHB][hapmap]
rs4653828	0.80[CHB][hapmap]
rs6690898	0.81[CHB][hapmap];0.81[YRI][hapmap]
rs7541775	0.81[CHB][hapmap]
rs7553358	0.81[YRI][hapmap]
rs7555764	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4294380	IMAGE3451454	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227576800-227584600	Weak transcription	A549	lung
2	chr1:227577000-227579000	Weak transcription	Stomach Mucosa	stomach
3	chr1:227577000-227579600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:227577000-227583200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:227577800-227583200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:227578400-227579800	Enhancers	K562	blood
7	chr1:227578400-227583200	Weak transcription	HSMMtube	muscle

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