Variant report

Variant	rs16998490
Chromosome Location	chr21:41160681-41160682
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	USF1	chr21:41160318-41160694	SK-N-SH_RA	brain:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
2	RAD21	chr21:41160122-41160835	SK-N-SH	brain:	n/a	chr21:41160401-41160420
3	SRF	chr21:41160250-41160928	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr21:41160214-41160748	T-47D	breast:	n/a	chr21:41160437-41160453
5	USF1	chr21:41160258-41160781	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
6	EP300	chr21:41160202-41161016	ECC-1	luminal epithelium:	n/a	chr21:41160437-41160453
7	MAX	chr21:41160258-41160851	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160538
8	SMC3	chr21:41160212-41160711	Hela-S3	cervix:	n/a	chr21:41160402-41160416
9	MXI1	chr21:41160113-41160862	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr21:41160293-41160866	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr21:41160292-41160823	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160538
12	CTCF	chr21:41160169-41160817	SK-N-SH	brain:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
13	EP300	chr21:41160211-41160872	ECC-1	luminal epithelium:	n/a	chr21:41160437-41160453
14	USF1	chr21:41160251-41160790	ECC-1	luminal epithelium:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
15	FOXM1	chr21:41160167-41160922	MCF-7	breast:	n/a	n/a
16	RAD21	chr21:41160033-41160861	MCF-7	breast:	n/a	chr21:41160401-41160420
17	SRF	chr21:41160290-41160924	ECC-1	luminal epithelium:	n/a	n/a
18	KAP1	chr21:41160155-41160791	U2OS	brain:	n/a	n/a
19	CTCF	chr21:41160147-41160748	HCT-116	colon:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
20	EP300	chr21:41160275-41160766	T-47D	breast:	n/a	chr21:41160437-41160453
21	CTCF	chr21:41160167-41160753	A549	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
22	TEAD4	chr21:41160245-41160681	H1-hESC	embryonic stem cell:	n/a	n/a
23	TEAD4	chr21:41160173-41160931	ECC-1	luminal epithelium:	n/a	n/a
24	RAD21	chr21:41160144-41160805	MCF-7	breast:	n/a	chr21:41160401-41160420
25	RAD21	chr21:41160167-41160704	A549	lung:	n/a	chr21:41160401-41160420
26	SIN3AK20	chr21:41160045-41160944	MCF-7	breast:	n/a	n/a
27	MAX	chr21:41160130-41160827	MCF-7	breast:	n/a	chr21:41160530-41160538
28	BHLHE40	chr21:41160279-41160720	HepG2	liver:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
29	CTCF	chr21:41160062-41160792	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
30	MAX	chr21:41160069-41160904	MCF-7	breast:	n/a	chr21:41160530-41160538
31	SMC3	chr21:41160170-41160703	SK-N-SH	brain:	n/a	chr21:41160402-41160416
32	RAD21	chr21:41160205-41160709	HCT-116	colon:	n/a	chr21:41160401-41160420
33	FOXA1	chr21:41160226-41160762	T-47D	breast:	n/a	n/a
34	USF1	chr21:41160335-41160795	HCT-116	colon:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
35	GATA3	chr21:41160217-41160802	T-47D	breast:	n/a	chr21:41160511-41160519
36	POLR2A	chr21:41160378-41160696	ECC-1	luminal epithelium:	n/a	n/a
37	ELF1	chr21:41160214-41160748	MCF-7	breast:	n/a	chr21:41160443-41160455
38	CUX1	chr21:41160393-41160762	K562	blood:	n/a	n/a
39	CTCF	chr21:41160215-41160747	T-47D	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
40	SRF	chr21:41160149-41160825	MCF-7	breast:	n/a	n/a
41	NFIC	chr21:41160157-41160861	ECC-1	luminal epithelium:	n/a	n/a
42	KAP1	chr21:41160107-41160801	HEK293	kidney:	n/a	n/a
43	RAD21	chr21:41160247-41160807	ECC-1	luminal epithelium:	n/a	chr21:41160401-41160420
44	CTCF	chr21:41160037-41160841	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
45	FOXA1	chr21:41160272-41160813	T-47D	breast:	n/a	n/a
46	NFIC	chr21:41160122-41160947	ECC-1	luminal epithelium:	n/a	n/a
47	RAD21	chr21:41160215-41160686	H1-hESC	embryonic stem cell:	n/a	chr21:41160401-41160420
48	FOXM1	chr21:41160140-41160904	ECC-1	luminal epithelium:	n/a	n/a
49	RAD21	chr21:41160093-41160855	ECC-1	luminal epithelium:	n/a	chr21:41160401-41160420
50	YY1	chr21:41160267-41160710	ECC-1	luminal epithelium:	n/a	chr21:41160443-41160457

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
ENSG00000183067	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000183036	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16998436	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998444	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16998519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16998532	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16998534	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998550	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998553	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998556	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16998576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17753538	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2837204	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs456303	0.99[ASN][1000 genomes]
rs55739464	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56955296	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67969662	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73215346	0.96[EUR][1000 genomes]
rs73217283	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73217284	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73217286	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73217292	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73217299	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73217300	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73219481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73219482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73219485	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73219486	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73219489	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73219490	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73219491	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73221250	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73904413	0.97[ASN][1000 genomes]
rs73904418	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73904443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8127368	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No data

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links