Variant report

Variant	rs9824325
Chromosome Location	chr3:53166510-53166511
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	RCOR1	chr3:53166506-53166687	HepG2	liver:	n/a	n/a
2	TCF7L2	chr3:53166371-53166620	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr3:53166264-53166813	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr3:53166310-53166731	HepG2	liver:	n/a	n/a
5	MXI1	chr3:53166391-53166609	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
2	chr3:53164535..53167069-chr3:53288219..53290615,2	MCF-7	breast:
3	chr3:53165904..53167414-chr3:53254063..53255573,2	MCF-7	breast:

Variant related genes	Relation type
RFT1	TF binding region
ENSG00000163931	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1004807	0.80[EUR][1000 genomes]
rs11130341	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12630819	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638996	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13319872	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13433700	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1560332	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2564929	0.88[ASN][1000 genomes]
rs2564944	0.87[EUR][1000 genomes]
rs28501212	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28734933	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796351	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4282053	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687570	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55950520	0.88[ASN][1000 genomes]
rs56058643	0.88[ASN][1000 genomes]
rs56386026	0.88[ASN][1000 genomes]
rs57261253	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57514626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61296683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62255925	0.88[ASN][1000 genomes]
rs62255926	0.81[ASN][1000 genomes]
rs62255929	0.88[ASN][1000 genomes]
rs62255931	0.88[ASN][1000 genomes]
rs6445565	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445566	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769931	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6769944	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777975	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6783748	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6784207	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792345	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792363	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6809973	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73088322	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73088327	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73088342	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7615099	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs891369	0.88[ASN][1000 genomes]
rs9757079	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9817467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9820125	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9820324	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830353	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838517	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9844531	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9845021	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9845352	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9845484	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858469	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9861744	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9867023	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9867590	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868263	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868406	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9872260	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878875	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9824325	RFT1	cis	Esophagus Muscularis	GTEx
rs9824325	RFT1	cis	Artery Aorta	GTEx
rs9824325	SERBP1P3	cis	Thyroid	GTEx
rs9824325	RFT1	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53164800-53170600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:53165000-53168600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:53165000-53169800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
6	chr3:53165200-53166600	Enhancers	A549	lung
7	chr3:53165200-53166800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:53165200-53167200	Enhancers	HMEC	breast
9	chr3:53165200-53169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:53165400-53167200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:53165400-53167600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:53165400-53168400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:53165400-53168600	Weak transcription	Colonic Mucosa	Colon
14	chr3:53165400-53168600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:53165400-53169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:53165400-53173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:53165400-53176000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:53165600-53167600	Weak transcription	Liver	Liver
19	chr3:53165600-53168400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:53165600-53168400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:53165600-53168400	Weak transcription	Hela-S3	cervix
22	chr3:53165600-53168400	Enhancers	HepG2	liver
23	chr3:53165600-53168600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:53165600-53168600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:53165600-53168600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:53165600-53168600	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:53165600-53168600	Weak transcription	Fetal Lung	lung
28	chr3:53165600-53168600	Weak transcription	Lung	lung
29	chr3:53165600-53168600	Weak transcription	Pancreas	Pancrea
30	chr3:53165600-53168600	Weak transcription	Right Ventricle	heart
31	chr3:53165600-53168600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:53165600-53168800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:53165600-53168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:53165600-53168800	Weak transcription	Esophagus	oesophagus
35	chr3:53165600-53169200	Weak transcription	Brain Anterior Caudate	brain
36	chr3:53165600-53169600	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:53165600-53170800	Weak transcription	Fetal Thymus	thymus
38	chr3:53165600-53173400	Weak transcription	Gastric	stomach
39	chr3:53165600-53174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:53165600-53174200	Weak transcription	Fetal Heart	heart
41	chr3:53165600-53174200	Weak transcription	Left Ventricle	heart
42	chr3:53165600-53174600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:53165600-53177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
45	chr3:53165800-53166600	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:53165800-53168400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:53165800-53168600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:53165800-53168600	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:53165800-53170600	Weak transcription	GM12878-XiMat	blood
50	chr3:53165800-53175400	Weak transcription	Placenta	Placenta

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