Variant report

Variant	rs58323492
Chromosome Location	chr1:62742865-62742866
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	chr1:62742429-62742927	MCF10A-Er-Src	breast:	n/a	chr1:62742590-62742597 chr1:62742590-62742599
2	FOS	chr1:62742441-62742872	MCF10A-Er-Src	breast:	n/a	chr1:62742590-62742597 chr1:62742590-62742599
3	FOS	chr1:62742417-62742927	MCF10A-Er-Src	breast:	n/a	chr1:62742590-62742597 chr1:62742590-62742599
4	STAT3	chr1:62742495-62742945	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
KANK4	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2886600	1.00[AMR][1000 genomes]
rs57413303	1.00[AMR][1000 genomes]
rs57469611	1.00[AMR][1000 genomes]
rs59107355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60767478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6656988	1.00[AMR][1000 genomes]
rs6657288	1.00[AMR][1000 genomes]
rs6673857	1.00[AMR][1000 genomes]
rs6697726	1.00[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:62734200-62750800	Weak transcription	Gastric	stomach
3	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
6	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:62739600-62744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:62740200-62746400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:62740400-62743200	Weak transcription	Liver	Liver
10	chr1:62740400-62744600	Weak transcription	Fetal Thymus	thymus
11	chr1:62740400-62745400	Weak transcription	Fetal Lung	lung
12	chr1:62740400-62746600	Weak transcription	Pancreas	Pancrea
13	chr1:62740600-62743000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:62740600-62744400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:62740600-62744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:62740600-62744600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:62741000-62745000	Weak transcription	HepG2	liver
18	chr1:62741200-62743200	Weak transcription	Fetal Stomach	stomach
19	chr1:62741200-62744400	Weak transcription	Fetal Heart	heart
20	chr1:62741800-62743000	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:62741800-62744600	Weak transcription	Placenta	Placenta
22	chr1:62742600-62743000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:62742600-62743200	Enhancers	HMEC	breast
24	chr1:62742600-62743200	Enhancers	NHEK	skin
25	chr1:62742600-62743400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:62742600-62743600	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr1:62742800-62743200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:62742800-62743400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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