Variant report

Variant	rs720844
Chromosome Location	chr2:149350128-149350129
allele	C/T
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	CEBPB	chr2:149350122-149350391	Hela-S3	cervix:	n/a	chr2:149350257-149350268 chr2:149350257-149350268 chr2:149350252-149350269
2	FOS	chr2:149350078-149350341	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:149349422..149353491-chr2:149401534..149405104,5	MCF-7	breast:
2	chr2:149348211..149350495-chr2:149361167..149362681,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232238	TF binding region
ENSG00000135999	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1020468	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1031290	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10454124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10928399	0.85[EUR][1000 genomes]
rs10928404	0.94[ASN][1000 genomes]
rs10928407	0.96[ASN][1000 genomes]
rs12464036	0.90[ASN][1000 genomes]
rs12472738	0.98[ASN][1000 genomes]
rs12619201	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13004738	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13010027	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16828836	0.93[ASN][1000 genomes]
rs16828954	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16828967	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16829006	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829034	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16829057	0.86[JPT][hapmap]
rs34210886	0.84[ASN][1000 genomes]
rs34671855	0.91[ASN][1000 genomes]
rs35057193	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35076661	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35154707	0.94[ASN][1000 genomes]
rs35168772	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36067597	0.94[ASN][1000 genomes]
rs4972285	0.93[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972369	0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4972375	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4972380	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972381	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972383	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430323	0.94[ASN][1000 genomes]
rs6709767	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6743835	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6746352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6761549	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs71413623	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7571333	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7578059	0.94[ASN][1000 genomes]
rs7590549	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7597133	0.94[ASN][1000 genomes]
rs7599758	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7606475	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs764386	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs930651	0.94[ASN][1000 genomes]
rs930652	0.94[ASN][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	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1000101	chr2:149165813-149361220	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs720844	NEB	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149343800-149350400	Weak transcription	Fetal Lung	lung
2	chr2:149348600-149350400	Weak transcription	NHEK	skin
3	chr2:149348600-149352000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:149349800-149350800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:149349800-149350800	Enhancers	Monocytes-CD14+_RO01746	blood

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