Variant report

Variant	rs3000787
Chromosome Location	chr1:227584832-227584833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227506125..227508936-chr1:227583007..227585460,2	K562	blood:
2	chr1:227581289..227584250-chr1:227584710..227586492,2	MCF-7	breast:
3	chr1:227583675..227585639-chr1:227602382..227605024,2	K562	blood:
4	chr1:227573402..227580584-chr1:227581981..227587587,10	K562	blood:
5	chr1:227583443..227586949-chr1:227620291..227624641,4	K562	blood:
6	chr1:227567329..227569359-chr1:227583309..227586812,3	K562	blood:

Variant related genes	Relation type
ENSG00000224834	Chromatin interaction
ENSG00000234277	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10082258	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12729548	0.82[AMR][1000 genomes]
rs3000775	1.00[CEU][hapmap]
rs3000778	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000779	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000781	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3000782	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000783	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000784	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000785	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3000786	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3000788	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3000789	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs3000792	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3000794	0.83[AMR][1000 genomes]
rs3000796	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3000797	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3000798	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3000804	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3000806	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs3000807	0.83[AMR][1000 genomes]
rs3000809	0.82[AMR][1000 genomes]
rs3000810	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3000811	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3000816	0.82[EUR][1000 genomes]
rs3014273	1.00[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs3014275	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3014277	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3014278	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3014279	1.00[CEU][hapmap]
rs3014280	1.00[CEU][hapmap]
rs3014287	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3014288	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3014290	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3014291	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3014292	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3014293	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3014295	0.84[AMR][1000 genomes]
rs3014296	0.84[AMR][1000 genomes]
rs3014297	0.84[AMR][1000 genomes]
rs3014298	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs3014299	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs3014300	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs3014301	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs3122560	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3122561	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3125124	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4468130	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4521965	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4570389	0.84[AMR][1000 genomes]
rs6670834	0.85[AMR][1000 genomes]
rs6697269	0.88[EUR][1000 genomes]
rs6699969	0.82[EUR][1000 genomes]
rs9426519	0.82[AMR][1000 genomes]
rs9426521	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs9426557	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv873243	chr1:227581017-227617519	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227580200-227585000	Weak transcription	HUVEC	blood vessel
2	chr1:227583600-227585400	Enhancers	Stomach Mucosa	stomach
3	chr1:227583600-227585400	Flanking Active TSS	K562	blood
4	chr1:227584200-227585200	Enhancers	Thymus	Thymus
5	chr1:227584200-227585400	Enhancers	Primary T cells from cord blood	blood
6	chr1:227584600-227585400	Enhancers	A549	lung
7	chr1:227584800-227585000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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