Variant report

Variant	rs10753427
Chromosome Location	chr1:223853727-223853728
allele	A/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	FOSL2	chr1:223853234-223853811	MCF-7	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
2	FOS	chr1:223853309-223854025	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
3	FOS	chr1:223853309-223854343	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
4	STAT3	chr1:223853429-223854335	MCF10A-Er-Src	breast:	n/a	chr1:223854169-223854180
5	FOS	chr1:223853321-223853941	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
6	GATA3	chr1:223853077-223853944	MCF-7	breast:	n/a	chr1:223853483-223853493 chr1:223853805-223853815
7	GATA3	chr1:223853196-223853938	MCF-7	breast:	n/a	chr1:223853483-223853493 chr1:223853805-223853815
8	MYC	chr1:223853438-223854310	MCF10A-Er-Src	breast:	n/a	n/a
9	SRF	chr1:223853085-223853862	MCF-7	breast:	n/a	n/a
10	STAT3	chr1:223853424-223854325	MCF10A-Er-Src	breast:	n/a	chr1:223854169-223854180
11	FOS	chr1:223853309-223854391	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
12	GATA3	chr1:223853252-223853771	T-47D	breast:	n/a	chr1:223853483-223853493
13	HDAC2	chr1:223853253-223853848	MCF-7	breast:	n/a	chr1:223853521-223853529
14	MYC	chr1:223853346-223853936	MCF10A-Er-Src	breast:	n/a	n/a
15	SIN3AK20	chr1:223853018-223853984	MCF-7	breast:	n/a	n/a
16	STAT3	chr1:223853408-223854347	MCF10A-Er-Src	breast:	n/a	chr1:223854169-223854180
17	FOSL2	chr1:223853230-223853796	MCF-7	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
18	ZNF217	chr1:223853235-223853791	MCF-7	breast:	n/a	n/a
19	STAT3	chr1:223853402-223853890	MCF10A-Er-Src	breast:	n/a	n/a
20	GATA3	chr1:223853075-223853870	MCF-7	breast:	n/a	chr1:223853483-223853493 chr1:223853805-223853815
21	NR2F2	chr1:223853120-223853862	MCF-7	breast:	n/a	n/a
22	NR2F2	chr1:223853200-223853814	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223831956..223833970-chr1:223853050..223855835,2	MCF-7	breast:
2	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:
3	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
4	chr1:223348196..223351831-chr1:223853498..223856683,4	MCF-7	breast:

Variant related genes	Relation type
CAPN8	TF binding region
ENSG00000203697	Chromatin interaction
ENSG00000227002	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10799364	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915854	1.00[AMR][1000 genomes]
rs10916015	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12021978	0.94[ASN][1000 genomes]
rs12025562	0.86[CHB][hapmap];0.92[GIH][hapmap]
rs12030569	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12031214	0.85[CHB][hapmap]
rs12032635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12034086	1.00[ASN][1000 genomes]
rs12036952	0.86[CHB][hapmap];0.92[GIH][hapmap]
rs12037022	0.99[ASN][1000 genomes]
rs12042187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12042337	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12132899	0.93[CHB][hapmap]
rs1222144	1.00[AMR][1000 genomes]
rs1361915	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1539703	1.00[AMR][1000 genomes]
rs16842210	1.00[AMR][1000 genomes]
rs16842251	1.00[AMR][1000 genomes]
rs1857549	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1892071	1.00[AMR][1000 genomes]
rs1892074	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs1892075	1.00[AMR][1000 genomes]
rs1977898	1.00[AMR][1000 genomes]
rs2000317	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2096343	1.00[AMR][1000 genomes]
rs2154115	1.00[AMR][1000 genomes]
rs2186005	1.00[AMR][1000 genomes]
rs2404288	1.00[AMR][1000 genomes]
rs25655	1.00[AMR][1000 genomes]
rs28370086	1.00[AMR][1000 genomes]
rs28370105	1.00[AMR][1000 genomes]
rs28370108	1.00[AMR][1000 genomes]
rs4653792	1.00[AMR][1000 genomes]
rs4653866	1.00[ASW][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653869	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6422641	1.00[AMR][1000 genomes]
rs6688648	1.00[AMR][1000 genomes]
rs7538151	1.00[AMR][1000 genomes]
rs7551783	0.81[ASN][1000 genomes]
rs7554290	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223851800-223857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:223853000-223853800	Enhancers	Esophagus	oesophagus
3	chr1:223853000-223853800	Enhancers	Pancreas	Pancrea
4	chr1:223853000-223854000	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:223853000-223854400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:223853000-223854600	Enhancers	Hela-S3	cervix
7	chr1:223853000-223855800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:223853200-223853800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:223853200-223853800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:223853200-223853800	Enhancers	Fetal Intestine Small	intestine
11	chr1:223853200-223853800	Enhancers	Placenta	Placenta
12	chr1:223853200-223854000	Enhancers	Fetal Intestine Large	intestine
13	chr1:223853200-223854600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:223853400-223854000	Enhancers	Colonic Mucosa	Colon
15	chr1:223853400-223854000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:223853400-223854200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:223853400-223855000	Weak transcription	Gastric	stomach
18	chr1:223853400-223856000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:223853400-223856600	Weak transcription	Lung	lung
20	chr1:223853400-223856800	Enhancers	HMEC	breast
21	chr1:223853400-223857000	Enhancers	Stomach Mucosa	stomach
22	chr1:223853600-223853800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:223853600-223853800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:223853600-223853800	Flanking Active TSS	NHEK	skin
25	chr1:223853600-223854000	Enhancers	A549	lung

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