Variant report

Variant	rs457024
Chromosome Location	chr21:41160601-41160602
allele	A/G
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	USF1	chr21:41160383-41160608	SK-N-SH	brain:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
2	USF1	chr21:41160318-41160694	SK-N-SH_RA	brain:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
3	USF1	chr21:41160414-41160611	HepG2	liver:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
4	RAD21	chr21:41160122-41160835	SK-N-SH	brain:	n/a	chr21:41160401-41160420
5	SRF	chr21:41160250-41160928	ECC-1	luminal epithelium:	n/a	n/a
6	STAT3	chr21:41160440-41160603	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr21:41160214-41160748	T-47D	breast:	n/a	chr21:41160437-41160453
8	USF1	chr21:41160258-41160781	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
9	EP300	chr21:41160202-41161016	ECC-1	luminal epithelium:	n/a	chr21:41160437-41160453
10	SMC3	chr21:41160219-41160623	HepG2	liver:	n/a	chr21:41160402-41160416
11	MAX	chr21:41160258-41160851	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160538
12	SMC3	chr21:41160212-41160711	Hela-S3	cervix:	n/a	chr21:41160402-41160416
13	MXI1	chr21:41160113-41160862	SK-N-SH	brain:	n/a	n/a
14	SMC3	chr21:41160248-41160617	K562	blood:	n/a	chr21:41160402-41160416
15	RAD21	chr21:41160148-41160655	SK-N-SH_RA	brain:	n/a	chr21:41160401-41160420
16	TCF12	chr21:41160293-41160866	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr21:41160267-41160622	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
18	MAX	chr21:41160292-41160823	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160538
19	CTCF	chr21:41160169-41160817	SK-N-SH	brain:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
20	EP300	chr21:41160211-41160872	ECC-1	luminal epithelium:	n/a	chr21:41160437-41160453
21	CTCF	chr21:41160243-41160601	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
22	RCOR1	chr21:41160242-41160621	K562	blood:	n/a	n/a
23	USF1	chr21:41160251-41160790	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
24	TEAD4	chr21:41160195-41160649	A549	lung:	n/a	n/a
25	FOXM1	chr21:41160167-41160922	MCF-7	breast:	n/a	n/a
26	RAD21	chr21:41160033-41160861	MCF-7	breast:	n/a	chr21:41160401-41160420
27	SRF	chr21:41160290-41160924	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr21:41160296-41160666	Hela-S3	cervix:	n/a	chr21:41160530-41160538
29	KAP1	chr21:41160155-41160791	U2OS	brain:	n/a	n/a
30	CTCF	chr21:41160147-41160748	HCT-116	colon:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
31	EP300	chr21:41160275-41160766	T-47D	breast:	n/a	chr21:41160437-41160453
32	CTCF	chr21:41160167-41160753	A549	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
33	TEAD4	chr21:41160245-41160681	H1-hESC	embryonic stem cell:	n/a	n/a
34	TEAD4	chr21:41160173-41160931	ECC-1	luminal epithelium:	n/a	n/a
35	USF1	chr21:41160349-41160615	HepG2	liver:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
36	RAD21	chr21:41160144-41160805	MCF-7	breast:	n/a	chr21:41160401-41160420
37	RAD21	chr21:41160167-41160704	A549	lung:	n/a	chr21:41160401-41160420
38	CTCF	chr21:41160262-41160637	T-47D	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
39	CTCF	chr21:41160256-41160601	A549	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
40	SIN3AK20	chr21:41160045-41160944	MCF-7	breast:	n/a	n/a
41	MAX	chr21:41160130-41160827	MCF-7	breast:	n/a	chr21:41160530-41160538
42	BHLHE40	chr21:41160279-41160720	HepG2	liver:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
43	CTCF	chr21:41160062-41160792	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
44	CTCF	chr21:41160183-41160658	H1-hESC	embryonic stem cell:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
45	MAX	chr21:41160069-41160904	MCF-7	breast:	n/a	chr21:41160530-41160538
46	SMC3	chr21:41160170-41160703	SK-N-SH	brain:	n/a	chr21:41160402-41160416
47	CTCF	chr21:41160213-41160644	K562	blood:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
48	CTCF	chr21:41160251-41160627	K562	blood:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
49	RAD21	chr21:41160205-41160709	HCT-116	colon:	n/a	chr21:41160401-41160420
50	CTCF	chr21:41160158-41160655	K562	blood:	n/a	chr21:41160400-41160418 chr21:41160402-41160423

No.	Distal block	Cell Line	Cell type
1	chr21:41160054..41160775-chr21:41284759..41285609,3	MCF-7	breast:
2	chr21:41160021..41160889-chr21:41227496..41228500,10	MCF-7	breast:
3	chr21:41159989..41160905-chr21:41238798..41240091,5	MCF-7	breast:
4	chr21:41160070..41160863-chr21:41223917..41224517,2	MCF-7	breast:
5	chr21:41097352..41098641-chr21:41159794..41160890,6	MCF-7	breast:
6	chr21:41159990..41160890-chr21:41235008..41236199,4	MCF-7	breast:
7	chr21:41160348..41160916-chr3:64008916..64009648,2	MCF-7	breast:
8	chr21:41160210..41160951-chr21:41226545..41227182,3	MCF-7	breast:
9	chr21:41159565..41161270-chr21:41282682..41284025,38	MCF-7	breast:
10	chr21:41160032..41160849-chr21:41490469..41491137,2	MCF-7	breast:
11	chr21:41160014..41161121-chr21:41238636..41239761,13	MCF-7	breast:
12	chr21:41159272..41160801-chr21:41162335..41164635,2	MCF-7	breast:
13	chr20:52556347..52557088-chr21:41160097..41160766,2	MCF-7	breast:
14	chr21:41159877..41161605-chr21:41224829..41226757,2	MCF-7	breast:
15	chr21:41159946..41160938-chr21:41279878..41281257,7	MCF-7	breast:
16	chr21:41160001..41160898-chr21:41492571..41493083,2	K562	blood:
17	chr21:41159912..41160982-chr21:41296603..41297482,6	MCF-7	breast:
18	chr21:41159761..41160935-chr21:41492511..41493448,9	MCF-7	breast:
19	chr21:41160024..41160878-chr21:41233096..41233742,2	MCF-7	breast:
20	chr21:41159981..41160860-chr21:41296870..41297616,2	MCF-7	breast:
21	chr21:41160023..41160863-chr21:41279931..41280819,2	MCF-7	breast:
22	chr21:41160053..41161081-chr21:41282734..41283845,12	MCF-7	breast:
23	chr21:41159987..41160858-chr21:41490256..41491059,2	MCF-7	breast:
24	chr21:41159989..41160876-chr21:41491630..41493536,21	MCF-7	breast:

Variant related genes	Relation type
IGSF5	TF binding region
ENSG00000163636	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000183067	Chromatin interaction
ENSG00000183036	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2837205	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837210	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs378814	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs456334	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs456685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461238	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs461503	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs463119	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs463652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781625	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56373284	1.00[ASN][1000 genomes]
rs7278863	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73219408	1.00[ASN][1000 genomes]
rs73219471	0.95[ASN][1000 genomes]
rs73219473	0.95[ASN][1000 genomes]
rs8128761	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9680296	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834099	chr21:41076873-41206030	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3329011	chr21:41158272-41160991	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs457024	PCP4	cis	Artery Tibial	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41156800-41160800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr21:41160000-41163600	Enhancers	Fetal Heart	heart
3	chr21:41160200-41160800	Enhancers	Rectal Smooth Muscle	rectum
4	chr21:41160200-41160800	Enhancers	Stomach Smooth Muscle	stomach
5	chr21:41160200-41161400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr21:41160400-41160800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:41160400-41160800	Active TSS	Brain Angular Gyrus	brain
8	chr21:41160400-41160800	Enhancers	Brain Germinal Matrix	brain
9	chr21:41160400-41160800	Active TSS	Brain Hippocampus Middle	brain
10	chr21:41160400-41160800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr21:41160400-41160800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr21:41160400-41160800	Active TSS	Fetal Brain Female	brain
13	chr21:41160400-41160800	Enhancers	Fetal Muscle Trunk	muscle
14	chr21:41160400-41160800	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr21:41160400-41160800	Active TSS	A549	lung
16	chr21:41160400-41160800	Enhancers	HMEC	breast
17	chr21:41160400-41161000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr21:41160400-41161000	Flanking Active TSS	Fetal Kidney	kidney
19	chr21:41160400-41161000	Enhancers	Fetal Muscle Leg	muscle
20	chr21:41160400-41161200	Active TSS	Right Ventricle	heart
21	chr21:41160400-41161400	Enhancers	Placenta	Placenta
22	chr21:41160600-41160800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:41160600-41160800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:41160600-41160800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr21:41160600-41160800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr21:41160600-41160800	Active TSS	Stomach Mucosa	stomach
27	chr21:41160600-41160800	Flanking Active TSS	NH-A	brain
28	chr21:41160600-41161000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr21:41160600-41161000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr21:41160600-41161000	Enhancers	Fetal Lung	lung
31	chr21:41160600-41161200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr21:41160600-41161200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr21:41160600-41161200	Enhancers	Fetal Stomach	stomach
34	chr21:41160600-41161200	Active TSS	Left Ventricle	heart
35	chr21:41160600-41161400	Enhancers	Pancreas	Pancrea
36	chr21:41160600-41161400	Active TSS	Right Atrium	heart
37	chr21:41160600-41163200	Weak transcription	Colon Smooth Muscle	Colon

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