Variant report

Variant	rs6033860
Chromosome Location	chr20:1448575-1448576
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	CUX1	chr20:1448299-1448712	K562	blood:	n/a	n/a
2	GTF2F1	chr20:1447333-1448934	K562	blood:	n/a	n/a
3	CTCF	chr20:1446644-1448611	A549	lung:	n/a	chr20:1447654-1447670 chr20:1447653-1447671
4	GATA3	chr20:1448013-1448652	T-47D	breast:	n/a	n/a
5	MAZ	chr20:1448265-1448621	HepG2	liver:	n/a	n/a
6	SMC3	chr20:1447500-1448649	HepG2	liver:	n/a	chr20:1447655-1447669
7	CEBPB	chr20:1448404-1448714	K562	blood:	n/a	n/a
8	MXI1	chr20:1448294-1448648	K562	blood:	n/a	n/a
9	MXI1	chr20:1446807-1448702	HepG2	liver:	n/a	n/a
10	ARID3A	chr20:1447389-1448758	HepG2	liver:	n/a	chr20:1447465-1447480
11	POLR2A	chr20:1447047-1449237	K562	blood:	n/a	n/a
12	POLR2A	chr20:1447018-1449457	NB4	blood:	n/a	n/a
13	UBTF	chr20:1448461-1448661	K562	blood:	n/a	n/a
14	ZNF143	chr20:1447404-1448872	K562	blood:	n/a	n/a
15	JUND	chr20:1448036-1449133	K562	blood:	n/a	n/a
16	UBTF	chr20:1448059-1448650	K562	blood:	n/a	n/a
17	RCOR1	chr20:1447322-1448629	K562	blood:	n/a	n/a
18	POLR2A	chr20:1446816-1449625	HL-60	blood:	n/a	n/a
19	NFYA	chr20:1448291-1448797	K562	blood:	n/a	chr20:1448567-1448585
20	E2F6	chr20:1448384-1448699	K562	blood:	n/a	n/a
21	BHLHE40	chr20:1447084-1448616	K562	blood:	n/a	chr20:1447494-1447510 chr20:1447574-1447590 chr20:1447087-1447103
22	TBP	chr20:1446839-1449132	K562	blood:	n/a	n/a
23	ZNF384	chr20:1447291-1448671	K562	blood:	n/a	n/a
24	GATA1	chr20:1446696-1448690	PBDE	blood:	n/a	n/a
25	EP300	chr20:1448447-1448697	HepG2	liver:	n/a	n/a
26	TEAD4	chr20:1448311-1448677	K562	blood:	n/a	n/a
27	E2F6	chr20:1447139-1449044	K562	blood:	n/a	chr20:1447465-1447480 chr20:1447305-1447315
28	CCNT2	chr20:1448086-1448714	K562	blood:	n/a	n/a
29	EP300	chr20:1448242-1448736	K562	blood:	n/a	n/a
30	RUNX3	chr20:1448367-1448705	GM12878	blood:	n/a	n/a
31	FOXA1	chr20:1448105-1448692	HepG2	liver:	n/a	n/a
32	POLR2A	chr20:1446889-1449085	HL-60	blood:	n/a	n/a
33	POLR2A	chr20:1448175-1448839	K562	blood:	n/a	n/a
34	PML	chr20:1448426-1449004	K562	blood:	n/a	n/a
35	TAL1	chr20:1448013-1449223	K562	blood:	n/a	n/a
36	POLR2A	chr20:1447001-1449309	K562	blood:	n/a	n/a
37	HCFC1	chr20:1447055-1448709	K562	blood:	n/a	n/a
38	MAX	chr20:1448260-1448834	K562	blood:	n/a	n/a
39	EP300	chr20:1447361-1448861	GM12878	blood:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
40	POLR2A	chr20:1446878-1448580	PBDE	blood:	n/a	n/a
41	MYC	chr20:1446965-1449011	NB4	blood:	n/a	chr20:1447602-1447611 chr20:1447606-1447613
42	TBP	chr20:1448254-1448838	HepG2	liver:	n/a	n/a
43	CBX3	chr20:1448267-1448821	K562	blood:	n/a	n/a
44	MAX	chr20:1446894-1448894	NB4	blood:	n/a	chr20:1447602-1447611 chr20:1447606-1447613
45	CEBPB	chr20:1448318-1448797	K562	blood:	n/a	n/a
46	POLR2A	chr20:1448158-1449116	K562	blood:	n/a	n/a
47	CHD2	chr20:1448324-1449089	K562	blood:	n/a	n/a
48	ELF1	chr20:1448018-1448702	K562	blood:	n/a	chr20:1448381-1448394
49	POLR2A	chr20:1445679-1448953	HepG2	liver:	n/a	n/a
50	POLR2A	chr20:1448305-1449451	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1304840..1306676-chr20:1447020..1448985,3	K562	blood:
2	chr20:1371233..1373934-chr20:1446935..1449162,2	K562	blood:
3	chr20:1372232..1375944-chr20:1446656..1450761,3	MCF-7	breast:
4	chr20:1304611..1307577-chr20:1447050..1450049,5	K562	blood:
5	chr20:1372434..1374768-chr20:1446935..1449052,2	K562	blood:

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

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1543423	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1884387	0.86[ASN][1000 genomes]
rs2143832	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2873565	0.87[ASN][1000 genomes]
rs3795134	0.85[JPT][hapmap]
rs3795135	0.80[JPT][hapmap]
rs6033867	0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6033901	0.88[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6033910	0.81[ASN][1000 genomes]
rs6033950	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs6042462	0.81[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6042499	0.87[ASN][1000 genomes]
rs6042500	0.89[ASN][1000 genomes]
rs6042592	0.88[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6042602	0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6074709	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6074715	0.90[JPT][hapmap]
rs6079277	0.87[ASN][1000 genomes]
rs6079288	0.86[ASN][1000 genomes]
rs6079289	0.88[ASN][1000 genomes]
rs6079294	0.88[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079302	0.86[ASN][1000 genomes]
rs6079325	0.88[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs6079330	0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6079336	0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6079354	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6079361	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6079362	0.81[ASN][1000 genomes]
rs6105234	0.81[ASN][1000 genomes]
rs6110169	0.85[ASN][1000 genomes]
rs6110207	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6110215	0.81[ASN][1000 genomes]
rs6110226	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6131543	0.87[ASN][1000 genomes]
rs6131553	0.85[ASN][1000 genomes]
rs6135033	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6135048	0.87[ASN][1000 genomes]
rs6135050	0.87[ASN][1000 genomes]
rs6135060	0.88[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6135061	0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6135062	0.85[ASN][1000 genomes]
rs6135063	0.84[ASN][1000 genomes]
rs6135064	0.83[ASN][1000 genomes]
rs6135068	0.84[ASN][1000 genomes]
rs6135069	0.84[ASN][1000 genomes]
rs6135080	0.84[ASN][1000 genomes]
rs6135089	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6135095	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6135105	0.81[ASN][1000 genomes]
rs963867	0.94[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6033860	FASTKD5	cis	cerebellum	SCAN
rs6033860	NSFL1C	cis	cerebellum	SCAN
rs6033860	NSFL1C	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1446800-1448600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr20:1446800-1449000	Active TSS	Brain Hippocampus Middle	brain
3	chr20:1447600-1448600	Enhancers	Lung	lung
4	chr20:1447600-1449000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr20:1447600-1449800	Weak transcription	Small Intestine	intestine
6	chr20:1447600-1450000	Weak transcription	Aorta	Aorta
7	chr20:1447800-1448600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr20:1447800-1448800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr20:1447800-1448800	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr20:1447800-1448800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr20:1447800-1448800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr20:1447800-1449000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr20:1447800-1449000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:1447800-1449000	Flanking Active TSS	Fetal Intestine Large	intestine
15	chr20:1447800-1449000	Flanking Active TSS	Fetal Intestine Small	intestine
16	chr20:1447800-1449000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr20:1447800-1449000	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr20:1447800-1449400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr20:1448000-1448600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr20:1448000-1448600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr20:1448000-1448800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr20:1448000-1449000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr20:1448000-1449400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr20:1448000-1449400	Weak transcription	NH-A	brain
25	chr20:1448000-1449600	Weak transcription	HSMM	muscle
26	chr20:1448000-1449600	Weak transcription	Osteobl	bone
27	chr20:1448000-1449800	Weak transcription	HSMMtube	muscle
28	chr20:1448000-1450200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:1448000-1450200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr20:1448000-1450200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:1448200-1448600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr20:1448200-1448600	Active TSS	Primary hematopoietic stem cells	blood
33	chr20:1448200-1448600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr20:1448200-1448600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr20:1448200-1448600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr20:1448200-1448600	Bivalent Enhancer	GM12878-XiMat	blood
37	chr20:1448200-1448800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr20:1448200-1448800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr20:1448200-1448800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr20:1448200-1448800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr20:1448200-1448800	Active TSS	Duodenum Mucosa	Duodenum
42	chr20:1448200-1449000	Active TSS	Colonic Mucosa	Colon
43	chr20:1448200-1449000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr20:1448200-1449400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr20:1448200-1449400	Weak transcription	Gastric	stomach
46	chr20:1448200-1449600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:1448200-1449600	Weak transcription	Liver	Liver
48	chr20:1448200-1449600	Weak transcription	HMEC	breast
49	chr20:1448200-1449600	Weak transcription	HUVEC	blood vessel
50	chr20:1448200-1449800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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