Variant report

Variant	rs6033858
Chromosome Location	chr20:1447670-1447671
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	POLR2A	chr20:1446867-1447684	HEK293	kidney:	n/a	n/a
2	TCF7L2	chr20:1447404-1447689	Hela-S3	cervix:	n/a	n/a
3	CEBPD	chr20:1447019-1447857	HepG2	liver:	n/a	n/a
4	GABPA	chr20:1447312-1447776	Hela-S3	cervix:	n/a	chr20:1447535-1447542
5	STAT5A	chr20:1447262-1447876	GM12878	blood:	n/a	n/a
6	NANOG	chr20:1447395-1447746	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr20:1447328-1447819	H1-hESC	embryonic stem cell:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
8	POLR2A	chr20:1447195-1447707	PFSK-1	brain:	n/a	n/a
9	FOS	chr20:1447591-1447689	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr20:1447580-1447730	GM12867	blood:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
11	CTCF	chr20:1447538-1447755	GM20000	blood:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
12	TBP	chr20:1446710-1447988	HepG2	liver:	n/a	n/a
13	GTF2F1	chr20:1447333-1448934	K562	blood:	n/a	n/a
14	POLR2A	chr20:1447304-1447798	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr20:1446644-1448611	A549	lung:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
16	REST	chr20:1447148-1447735	PFSK-1	brain:	n/a	n/a
17	YY1	chr20:1446901-1447796	A549	lung:	n/a	chr20:1447459-1447479 chr20:1447590-1447601 chr20:1447522-1447533 chr20:1447090-1447101
18	EP300	chr20:1447067-1448184	HepG2	liver:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
19	ZNF143	chr20:1447343-1447816	H1-hESC	embryonic stem cell:	n/a	n/a
20	BCLAF1	chr20:1447252-1447850	GM12878	blood:	n/a	chr20:1447283-1447296 chr20:1447643-1447656 chr20:1447496-1447509 chr20:1447346-1447359 chr20:1447590-1447603 chr20:1447521-1447534
21	CTCF	chr20:1447600-1447750	BJ	skin:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
22	POLR2A	chr20:1446943-1447747	Gliobla	brain:	n/a	n/a
23	POLR2A	chr20:1446968-1447716	MCF-7	breast:	n/a	n/a
24	CTCF	chr20:1447540-1447690	SAEC	small airway:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
25	SP4	chr20:1447337-1448015	H1-hESC	embryonic stem cell:	n/a	chr20:1447596-1447607
26	HNF4G	chr20:1447299-1447765	HepG2	liver:	n/a	n/a
27	ETS1	chr20:1447174-1447739	GM12878	blood:	n/a	chr20:1447696-1447709
28	ELK1	chr20:1447326-1447726	GM12878	blood:	n/a	n/a
29	IRF1	chr20:1447290-1447695	K562	blood:	n/a	chr20:1447594-1447608
30	SMC3	chr20:1447500-1448649	HepG2	liver:	n/a	chr20:1447655-1447669
31	CTCF	chr20:1447320-1447818	H1-hESC	embryonic stem cell:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
32	TEAD4	chr20:1447353-1447736	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr20:1447600-1447750	HPAF	blood vessel:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
34	CTCF	chr20:1447520-1447670	HA-sp	spinal cord:	n/a	chr20:1447654-1447670
35	CTCF	chr20:1447301-1447969	HCT-116	colon:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
36	RFX5	chr20:1447359-1447712	GM12878	blood:	n/a	n/a
37	TCF3	chr20:1447356-1447731	GM12878	blood:	n/a	n/a
38	TAF1	chr20:1447333-1447746	SK-N-SH	brain:	n/a	n/a
39	CHD2	chr20:1447046-1447844	GM12878	blood:	n/a	n/a
40	MAFK	chr20:1447029-1447782	HepG2	liver:	n/a	n/a
41	CBX3	chr20:1447112-1447964	HCT-116	colon:	n/a	n/a
42	RCOR1	chr20:1447132-1447940	GM12878	blood:	n/a	n/a
43	GABPA	chr20:1447072-1447750	HepG2	liver:	n/a	chr20:1447535-1447542
44	SRF	chr20:1447319-1447829	ECC-1	luminal epithelium:	n/a	chr20:1447598-1447608 chr20:1447327-1447337
45	CTCF	chr20:1447580-1447730	GM12870	blood:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
46	MXI1	chr20:1446807-1448702	HepG2	liver:	n/a	n/a
47	MAX	chr20:1447063-1447759	A549	lung:	n/a	chr20:1447602-1447611 chr20:1447606-1447613
48	TCF12	chr20:1447110-1447937	ECC-1	luminal epithelium:	n/a	n/a
49	CTCF	chr20:1447430-1447793	MCF-7	breast:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
50	CTCF	chr20:1447600-1447750	HRPEpiC	eye:	n/a	chr20:1447654-1447670 chr20:1447653-1447671

No.	Distal block	Cell Line	Cell type
1	chr20:1446155..1447724-chr20:1468382..1469913,2	MCF-7	breast:
2	chr20:1304840..1306676-chr20:1447020..1448985,3	K562	blood:
3	chr20:1306070..1308541-chr20:1446001..1448028,2	MCF-7	breast:
4	chr20:1371233..1373934-chr20:1446935..1449162,2	K562	blood:
5	chr20:1437321..1440209-chr20:1445376..1448458,3	MCF-7	breast:
6	chr20:1372232..1375944-chr20:1446656..1450761,3	MCF-7	breast:
7	chr20:1447017..1447769-chr9:102583969..102584507,2	Hela-S3	cervix:
8	chr20:1304611..1307577-chr20:1447050..1450049,5	K562	blood:
9	chr20:1372434..1374768-chr20:1446935..1449052,2	K562	blood:
10	chr20:1436244..1441221-chr20:1444525..1448562,4	MCF-7	breast:

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000088832	Chromatin interaction
ENSG00000266085	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000119508	Chromatin interaction
ENSG00000088833	Chromatin interaction
ENSG00000234684	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3795134	0.86[ASN][1000 genomes]
rs3795135	0.87[ASN][1000 genomes]
rs6074631	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv3375230	chr20:1446177-1448725	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1445800-1447800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr20:1446000-1447800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr20:1446200-1447800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr20:1446200-1447800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr20:1446200-1448000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr20:1446200-1448000	Active TSS	Fetal Muscle Trunk	muscle
7	chr20:1446400-1447800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:1446600-1447800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr20:1446600-1447800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:1446600-1447800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr20:1446600-1447800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:1446600-1447800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr20:1446600-1447800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:1446600-1447800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr20:1446600-1447800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:1446600-1447800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr20:1446600-1447800	Active TSS	Fetal Intestine Large	intestine
18	chr20:1446600-1447800	Active TSS	Pancreas	Pancrea
19	chr20:1446600-1447800	Active TSS	Right Atrium	heart
20	chr20:1446600-1447800	Active TSS	A549	lung
21	chr20:1446600-1447800	Active TSS	HSMM	muscle
22	chr20:1446600-1447800	Active TSS	NHDF-Ad	bronchial
23	chr20:1446600-1447800	Active TSS	NHLF	lung
24	chr20:1446600-1448000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr20:1446600-1448000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:1446600-1448000	Active TSS	Left Ventricle	heart
27	chr20:1446600-1448000	Active TSS	Psoas Muscle	Psoas
28	chr20:1446600-1448200	Active TSS	Gastric	stomach
29	chr20:1446800-1447800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr20:1446800-1447800	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr20:1446800-1447800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr20:1446800-1447800	Active TSS	Brain Angular Gyrus	brain
33	chr20:1446800-1447800	Active TSS	Brain Anterior Caudate	brain
34	chr20:1446800-1447800	Active TSS	Brain Cingulate Gyrus	brain
35	chr20:1446800-1447800	Active TSS	Brain Substantia Nigra	brain
36	chr20:1446800-1447800	Active TSS	Colonic Mucosa	Colon
37	chr20:1446800-1447800	Active TSS	Colon Smooth Muscle	Colon
38	chr20:1446800-1447800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr20:1446800-1447800	Active TSS	Fetal Intestine Small	intestine
40	chr20:1446800-1447800	Active TSS	Fetal Muscle Leg	muscle
41	chr20:1446800-1447800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr20:1446800-1447800	Active TSS	Right Ventricle	heart
43	chr20:1446800-1447800	Active TSS	Stomach Mucosa	stomach
44	chr20:1446800-1447800	Active TSS	Dnd41	blood
45	chr20:1446800-1447800	Active TSS	GM12878-XiMat	blood
46	chr20:1446800-1447800	Active TSS	Hela-S3	cervix
47	chr20:1446800-1447800	Bivalent/Poised TSS	HepG2	liver
48	chr20:1446800-1447800	Active TSS	NHEK	skin
49	chr20:1446800-1448000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr20:1446800-1448000	Active TSS	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links