Variant report

Variant	rs7552220
Chromosome Location	chr1:152479716-152479717
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	FOS	chr1:152479540-152479979	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:152479556-152479866	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F4	chr1:152479477-152479817	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr1:152479529-152479950	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:152479670-152479870	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:152479498-152480038	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:152479509-152479975	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr1:152479513-152479944	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr1:152479514-152479941	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:152479500-152480058	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr1:152479547-152479967	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr1:152479524-152479857	A549	lung:	n/a	n/a
13	FOS	chr1:152479529-152479990	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr1:152479553-152479975	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr1:152479431-152479933	A549	lung:	n/a	n/a
16	NR3C1	chr1:152479460-152479973	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152478290..152479934-chr1:152485097..152487214,2	MCF-7	breast:
2	chr1:152475128..152477150-chr1:152479048..152480719,2	MCF-7	breast:

Variant related genes	Relation type
LCE5A	TF binding region
ENSG00000169509	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1199154	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1199155	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1199157	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12563567	0.86[ASN][1000 genomes]
rs12568980	0.86[ASN][1000 genomes]
rs1577819	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16834087	1.00[JPT][hapmap]
rs16834142	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16834145	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16834153	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16834168	0.94[GIH][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1923508	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1984725	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297760	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587678	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6662563	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513266	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521139	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521224	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544342	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548813	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1014393	chr1:152451935-152491693	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2750810	chr1:152453669-152660927	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1012908	chr1:152464844-152517845	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1005553	chr1:152464844-152519197	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv547859	chr1:152466882-152482587	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013357	chr1:152469744-152519184	Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1798404	chr1:152472839-152587113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1827111	chr1:152472839-152690073	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1830764	chr1:152472839-152690073	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152473200-152480600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:152473600-152480200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152473800-152480600	Enhancers	HMEC	breast
4	chr1:152475400-152480600	Enhancers	NHEK	skin
5	chr1:152476400-152482400	Weak transcription	A549	lung
6	chr1:152478800-152480400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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