Variant report

Variant	rs3006423
Chromosome Location	chr1:153401664-153401665
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	CTCF	chr1:153401600-153401750	A549	lung:	n/a	n/a
2	CTCF	chr1:153401310-153401684	H1-hESC	embryonic stem cell:	n/a	chr1:153401483-153401496
3	CTCF	chr1:153401600-153401750	BE2_C	brain:	n/a	n/a
4	CTCF	chr1:153401580-153401730	HCM	heart:	n/a	n/a
5	RAD21	chr1:153401284-153401690	H1-hESC	embryonic stem cell:	n/a	chr1:153401486-153401496 chr1:153401486-153401498 chr1:153401481-153401500
6	CTCF	chr1:153401380-153401686	K562	blood:	n/a	chr1:153401483-153401496

No.	Distal block	Cell Line	Cell type
1	chr1:153365407..153367710-chr1:153401211..153403404,2	MCF-7	breast:
2	chr1:153401442..153403093-chr1:153408398..153410070,2	MCF-7	breast:
3	chr1:153401556..153403433-chr1:153405617..153407706,2	K562	blood:
4	chr1:153397872..153400976-chr1:153401654..153403402,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203781	TF binding region
ENSG00000203781	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10127752	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888560	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11205297	0.90[GIH][hapmap]
rs12022550	0.88[CHB][hapmap]
rs12034788	0.84[ASN][1000 genomes]
rs12036701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043280	0.88[GIH][hapmap];0.84[MEX][hapmap]
rs12043556	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs12044491	0.83[ASN][1000 genomes]
rs12045252	0.81[ASN][1000 genomes]
rs12047494	0.80[CHB][hapmap]
rs16835308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs16835332	0.80[CHB][hapmap]
rs2986209	0.80[CHB][hapmap]
rs3006412	0.90[CHB][hapmap]
rs3006413	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3006414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3006416	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3006422	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014813	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014814	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014815	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014816	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014817	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014823	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014848	0.84[CHB][hapmap]
rs41265152	0.83[ASN][1000 genomes]
rs4507965	1.00[ASN][1000 genomes]
rs4845348	1.00[CHB][hapmap]
rs72708746	0.83[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3355423	chr1:153401528-153405726	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153401400-153403400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153401600-153402200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin

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