Variant report

Variant	rs11162455
Chromosome Location	chr1:78769242-78769243
allele	A/C
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	GATA3	chr1:78769187-78769764	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr1:78769030-78769802	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:78769035-78769785	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:78769150-78769686	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:78769089-78770223	MCF10A-Er-Src	breast:	n/a	chr1:78769521-78769532
6	STAT3	chr1:78768918-78769854	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr1:78769173-78769823	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr1:78769236-78769680	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr1:78769235-78769860	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr1:78769151-78769824	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr1:78769200-78769715	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:78769179-78769718	U87	brain:	n/a	n/a
13	GATA3	chr1:78769085-78769818	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr1:78769185-78769712	U87	brain:	n/a	n/a
15	NFIC	chr1:78769237-78769819	SK-N-SH	brain:	n/a	n/a
16	JUND	chr1:78769193-78769769	SK-N-SH	brain:	n/a	n/a
17	FOS	chr1:78769227-78769820	MCF10A-Er-Src	breast:	n/a	chr1:78769521-78769532
18	FOSL2	chr1:78769193-78769824	SK-N-SH	brain:	n/a	n/a
19	EP300	chr1:78769144-78769829	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
PTGFR	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004435	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10489948	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873970	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873971	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162444	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162445	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162447	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11162448	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162449	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162450	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162452	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11804180	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11804577	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032466	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12035240	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036413	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12036778	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12041099	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12072800	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12076370	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12082822	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12728306	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1328443	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1328444	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1328445	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1417102	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1927779	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1952363	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35271660	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4650394	0.90[EUR][1000 genomes]
rs56729185	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674660	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6686438	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67402345	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7529466	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539904	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545766	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553079	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7553618	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78758400-78769400	Weak transcription	Pancreas	Pancrea
2	chr1:78767800-78770200	Enhancers	NHDF-Ad	bronchial
3	chr1:78768800-78769600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:78768800-78769800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:78768800-78770200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:78768800-78770400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:78768800-78770600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:78768800-78770600	Enhancers	Osteobl	bone
9	chr1:78768800-78770800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:78768800-78771000	Enhancers	NHLF	lung
11	chr1:78768800-78771200	Enhancers	Hela-S3	cervix
12	chr1:78769000-78770200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:78769000-78770200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:78769200-78769400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:78769200-78769600	Enhancers	NH-A	brain
16	chr1:78769200-78770000	Enhancers	Adipose Nuclei	Adipose
17	chr1:78769200-78770000	Enhancers	HSMM	muscle
18	chr1:78769200-78770000	Enhancers	NHEK	skin
19	chr1:78769200-78770600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:78769200-78770600	Enhancers	HMEC	breast

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