Variant report

Variant	rs72703449
Chromosome Location	chr9:21528954-21528955
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	POLR2A	chr9:21519358-21529034	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr9:21526622-21528964	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:21528725-21529335	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr9:21515900-21530251	A549	lung:	n/a	n/a
5	POLR2A	chr9:21528564-21529751	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr9:21516566-21534519	HCT-116	colon:	n/a	n/a
7	POLR2A	chr9:21519394-21529027	HCT-116	colon:	n/a	n/a
8	POLR2A	chr9:21528660-21529002	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000264379	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10491567	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811549	0.89[EUR][1000 genomes]
rs10811551	0.87[EUR][1000 genomes]
rs10811556	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811557	0.87[AMR][1000 genomes]
rs10811562	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811563	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811565	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10811566	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10811568	0.94[ASN][1000 genomes]
rs10965019	0.82[EUR][1000 genomes]
rs10965024	0.82[EUR][1000 genomes]
rs10965031	0.87[EUR][1000 genomes]
rs10965034	0.82[EUR][1000 genomes]
rs10965036	0.82[EUR][1000 genomes]
rs10965049	0.96[ASN][1000 genomes]
rs10965050	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965053	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10965054	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10965059	0.95[EUR][1000 genomes]
rs10965060	0.85[ASN][1000 genomes]
rs10965063	0.89[EUR][1000 genomes]
rs1125488	0.84[EUR][1000 genomes]
rs12375583	0.82[EUR][1000 genomes]
rs12377379	0.95[EUR][1000 genomes]
rs12378286	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12378990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12379382	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12379709	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12379721	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1332188	0.82[EUR][1000 genomes]
rs16938433	0.82[EUR][1000 genomes]
rs16938435	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16938448	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2039380	0.85[EUR][1000 genomes]
rs55683539	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55835613	0.95[EUR][1000 genomes]
rs56122777	0.95[EUR][1000 genomes]
rs56337511	0.82[EUR][1000 genomes]
rs7026731	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7032680	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7041183	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72703410	0.80[EUR][1000 genomes]
rs72703411	0.87[EUR][1000 genomes]
rs72703417	0.82[EUR][1000 genomes]
rs72703418	0.82[EUR][1000 genomes]
rs72703419	0.82[EUR][1000 genomes]
rs72703426	0.82[EUR][1000 genomes]
rs72703442	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72703445	0.95[EUR][1000 genomes]
rs72703447	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72703448	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72703450	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9644855	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:21508000-21542000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:21516800-21542600	Weak transcription	Stomach Mucosa	stomach
4	chr9:21522600-21532600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:21522600-21533200	Strong transcription	NH-A	brain
6	chr9:21522800-21530000	ZNF genes & repeats	A549	lung
7	chr9:21524400-21532200	Strong transcription	Osteobl	bone
8	chr9:21525600-21534000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:21525800-21530800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr9:21526200-21532400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:21526400-21529600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:21526400-21530000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:21526400-21534800	Strong transcription	NHEK	skin
14	chr9:21526600-21529000	Strong transcription	HUVEC	blood vessel
15	chr9:21526600-21530200	Strong transcription	HSMM	muscle
16	chr9:21526600-21533000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:21526800-21534800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:21527000-21531000	Strong transcription	NHDF-Ad	bronchial
19	chr9:21527000-21531200	Strong transcription	NHLF	lung
20	chr9:21527400-21529800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:21527600-21529000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:21527600-21529000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:21527600-21529000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:21527600-21529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:21527800-21529000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:21527800-21536600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:21528200-21529400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:21528200-21531600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr9:21528200-21532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:21528400-21529000	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr9:21528400-21530000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:21528600-21529000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:21528600-21531800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:21528800-21529000	Genic enhancers	Esophagus	oesophagus
35	chr9:21528800-21529600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:21528800-21530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:21528800-21530800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:21528800-21531000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:21528800-21532200	Strong transcription	HMEC	breast
40	chr9:21528800-21533000	Strong transcription	Hela-S3	cervix
41	chr9:21528800-21533400	Weak transcription	Fetal Intestine Large	intestine
42	chr9:21528800-21535800	Weak transcription	Gastric	stomach
43	chr9:21528800-21542000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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