Variant report

Variant	rs11196729
Chromosome Location	chr10:116167871-116167872
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	POLR2A	chr10:116167773-116168348	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr10:116167262-116169152	ECC-1	luminal epithelium:	n/a	chr10:116168256-116168270 chr10:116168151-116168161 chr10:116167884-116167900
3	MAX	chr10:116167438-116169270	ECC-1	luminal epithelium:	n/a	chr10:116168349-116168358 chr10:116168347-116168357 chr10:116168330-116168339
4	TCF12	chr10:116167700-116169141	ECC-1	luminal epithelium:	n/a	chr10:116168120-116168127 chr10:116168558-116168566
5	TCF12	chr10:116167718-116169187	ECC-1	luminal epithelium:	n/a	chr10:116168120-116168127 chr10:116168558-116168566
6	MAX	chr10:116167734-116169045	ECC-1	luminal epithelium:	n/a	chr10:116168349-116168358 chr10:116168347-116168357 chr10:116168330-116168339

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116162254..116164533-chr10:116167169..116169153,2	MCF-7	breast:

Variant related genes	Relation type
AFAP1L2	TF binding region
ENSG00000169129	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10885559	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885563	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10885566	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11196723	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4751903	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4752697	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs490607	0.84[EUR][1000 genomes]
rs7089635	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116165000-116172000	Weak transcription	Esophagus	oesophagus
2	chr10:116165000-116172600	Weak transcription	Pancreas	Pancrea
3	chr10:116165400-116172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr10:116166000-116168800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:116167400-116168600	Enhancers	GM12878-XiMat	blood
6	chr10:116167600-116168000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr10:116167600-116168000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:116167600-116168000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:116167600-116168000	Bivalent Enhancer	Fetal Thymus	thymus
10	chr10:116167600-116168200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
11	chr10:116167600-116168200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr10:116167600-116168200	Enhancers	NHEK	skin
13	chr10:116167600-116168600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr10:116167600-116169200	Enhancers	A549	lung
15	chr10:116167600-116169400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:116167600-116169600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:116167600-116169600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:116167600-116169800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr10:116167600-116170000	Enhancers	Spleen	Spleen
20	chr10:116167800-116169400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr10:116167800-116169400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:116167800-116170200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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