Variant report

Variant	rs6445565
Chromosome Location	chr3:53165464-53165465
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	IRF1	chr3:53164209-53165482	K562	blood:	n/a	chr3:53164525-53164539 chr3:53164649-53164658
2	POLR2A	chr3:53163223-53165663	PBDE	blood:	n/a	n/a
3	RCOR1	chr3:53164139-53165494	K562	blood:	n/a	n/a
4	CBX3	chr3:53164731-53165515	K562	blood:	n/a	n/a
5	FOSL2	chr3:53165146-53165560	HepG2	liver:	n/a	chr3:53165377-53165387 chr3:53165377-53165387 chr3:53165377-53165386 chr3:53165377-53165387 chr3:53165377-53165387 chr3:53165376-53165388 chr3:53165379-53165390
6	BHLHE40	chr3:53163025-53165493	K562	blood:	n/a	n/a
7	RCOR1	chr3:53164200-53165509	K562	blood:	n/a	n/a
8	JUND	chr3:53164201-53165554	K562	blood:	n/a	chr3:53165377-53165387 chr3:53165377-53165387 chr3:53165377-53165386 chr3:53165376-53165387 chr3:53165377-53165387 chr3:53164525-53164534 chr3:53165377-53165387 chr3:53165376-53165388 chr3:53165379-53165390
9	POLR2A	chr3:53163320-53165471	K562	blood:	n/a	n/a
10	NR2F2	chr3:53165029-53165533	K562	blood:	n/a	n/a
11	POLR2A	chr3:53164180-53165587	K562	blood:	n/a	n/a
12	MAZ	chr3:53164221-53165509	K562	blood:	n/a	n/a
13	JUND	chr3:53165248-53165529	HepG2	liver:	n/a	chr3:53165377-53165387 chr3:53165377-53165387 chr3:53165377-53165386 chr3:53165376-53165387 chr3:53165377-53165387 chr3:53165377-53165387 chr3:53165376-53165388 chr3:53165379-53165390
14	MYC	chr3:53163031-53165499	K562	blood:	n/a	n/a
15	GATA1	chr3:53162990-53165732	PBDE	blood:	n/a	chr3:53163999-53164009 chr3:53164027-53164034 chr3:53163508-53163515
16	ATF1	chr3:53165092-53165516	K562	blood:	n/a	n/a
17	POLR2A	chr3:53162290-53165916	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:53165147-53165509	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	chr3:53163608..53165597-chr3:53189002..53191742,3	K562	blood:
3	chr3:53163489..53166052-chr3:53379929..53382792,2	K562	blood:
4	chr3:53164535..53167069-chr3:53288219..53290615,2	MCF-7	breast:

Variant related genes	Relation type
RFT1	TF binding region
ENSG00000163931	Chromatin interaction
ENSG00000163932	Chromatin interaction
ENSG00000162290	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	0.81[EUR][1000 genomes]
rs11130341	0.94[EUR][1000 genomes]
rs12630819	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12638996	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319872	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13433700	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1560332	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564929	0.91[ASN][1000 genomes]
rs2564944	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28501212	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734933	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796351	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4282053	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687570	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55950520	0.91[ASN][1000 genomes]
rs56058643	0.91[ASN][1000 genomes]
rs56386026	0.91[ASN][1000 genomes]
rs57261253	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57514626	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61296683	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255925	0.91[ASN][1000 genomes]
rs62255926	0.83[ASN][1000 genomes]
rs62255929	0.91[ASN][1000 genomes]
rs62255931	0.91[ASN][1000 genomes]
rs6445566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769931	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769944	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777975	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783748	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784207	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792363	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799837	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809973	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73088322	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088327	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088342	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615099	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891369	0.91[ASN][1000 genomes]
rs9757079	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817467	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820125	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820324	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824325	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828221	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830353	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834111	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838517	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844531	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9845021	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9845352	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845484	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858469	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861744	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9867023	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867590	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868263	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868406	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872260	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878875	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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
rs6445565	RFT1	cis	Esophagus Muscularis	GTEx
rs6445565	SERBP1P3	cis	Thyroid	GTEx
rs6445565	RFT1	cis	Artery Aorta	GTEx
rs6445565	RFT1	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53164000-53165600	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr3:53164600-53165600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:53164600-53165600	Flanking Active TSS	Fetal Lung	lung
4	chr3:53164600-53165600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr3:53164600-53165600	Flanking Active TSS	NHEK	skin
6	chr3:53164600-53166000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr3:53164600-53166000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:53164800-53165600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:53164800-53165600	Enhancers	Spleen	Spleen
10	chr3:53164800-53165600	Flanking Active TSS	Dnd41	blood
11	chr3:53164800-53165800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr3:53164800-53170600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:53165000-53165600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:53165000-53165600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:53165000-53165600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:53165000-53165600	Enhancers	Esophagus	oesophagus
17	chr3:53165000-53165600	Enhancers	Fetal Heart	heart
18	chr3:53165000-53165600	Enhancers	Gastric	stomach
19	chr3:53165000-53165600	Enhancers	Left Ventricle	heart
20	chr3:53165000-53165600	Enhancers	Lung	lung
21	chr3:53165000-53165600	Enhancers	Pancreas	Pancrea
22	chr3:53165000-53165600	Enhancers	Right Ventricle	heart
23	chr3:53165000-53165600	Flanking Active TSS	HepG2	liver
24	chr3:53165000-53165600	Flanking Active TSS	HSMM	muscle
25	chr3:53165000-53165600	Enhancers	NH-A	brain
26	chr3:53165000-53165800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:53165000-53165800	Enhancers	Placenta	Placenta
28	chr3:53165000-53165800	Enhancers	Right Atrium	heart
29	chr3:53165000-53165800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:53165000-53168600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:53165000-53169800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
34	chr3:53165200-53165600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:53165200-53165600	Enhancers	Primary B cells from peripheral blood	blood
36	chr3:53165200-53165600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:53165200-53165600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:53165200-53165600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:53165200-53165600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:53165200-53165600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:53165200-53165600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:53165200-53165600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:53165200-53165600	Enhancers	Brain Anterior Caudate	brain
44	chr3:53165200-53165600	Enhancers	Brain Cingulate Gyrus	brain
45	chr3:53165200-53165600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr3:53165200-53165600	Enhancers	Brain Substantia Nigra	brain
47	chr3:53165200-53165600	Enhancers	Colon Smooth Muscle	Colon
48	chr3:53165200-53165600	Enhancers	Fetal Intestine Small	intestine
49	chr3:53165200-53165600	Enhancers	Fetal Kidney	kidney
50	chr3:53165200-53165600	Enhancers	Fetal Thymus	thymus

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