Variant report

Variant	rs6135033
Chromosome Location	chr20:1448366-1448367
allele	G/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	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	FOXA1	chr20:1448296-1448505	T-47D	breast:	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	ZNF143	chr20:1447404-1448872	K562	blood:	n/a	n/a
14	JUND	chr20:1448036-1449133	K562	blood:	n/a	n/a
15	UBTF	chr20:1448059-1448650	K562	blood:	n/a	n/a
16	RCOR1	chr20:1447322-1448629	K562	blood:	n/a	n/a
17	POLR2A	chr20:1446816-1449625	HL-60	blood:	n/a	n/a
18	NFYA	chr20:1448291-1448797	K562	blood:	n/a	chr20:1448567-1448585
19	BHLHE40	chr20:1447084-1448616	K562	blood:	n/a	chr20:1447494-1447510 chr20:1447574-1447590 chr20:1447087-1447103
20	TBP	chr20:1446839-1449132	K562	blood:	n/a	n/a
21	ZNF384	chr20:1447291-1448671	K562	blood:	n/a	n/a
22	GATA1	chr20:1446696-1448690	PBDE	blood:	n/a	n/a
23	MBD4	chr20:1446951-1448473	HepG2	liver:	n/a	n/a
24	TEAD4	chr20:1448311-1448677	K562	blood:	n/a	n/a
25	E2F6	chr20:1447139-1449044	K562	blood:	n/a	chr20:1447465-1447480 chr20:1447305-1447315
26	CCNT2	chr20:1448086-1448714	K562	blood:	n/a	n/a
27	EP300	chr20:1448242-1448736	K562	blood:	n/a	n/a
28	FOXA1	chr20:1448105-1448692	HepG2	liver:	n/a	n/a
29	POLR2A	chr20:1446889-1449085	HL-60	blood:	n/a	n/a
30	POLR2A	chr20:1448175-1448839	K562	blood:	n/a	n/a
31	TAL1	chr20:1448013-1449223	K562	blood:	n/a	n/a
32	POLR2A	chr20:1447001-1449309	K562	blood:	n/a	n/a
33	HCFC1	chr20:1447055-1448709	K562	blood:	n/a	n/a
34	MAX	chr20:1448260-1448834	K562	blood:	n/a	n/a
35	EP300	chr20:1447361-1448861	GM12878	blood:	n/a	chr20:1447501-1447510 chr20:1447499-1447508 chr20:1447573-1447589
36	POLR2A	chr20:1446878-1448580	PBDE	blood:	n/a	n/a
37	MYC	chr20:1446965-1449011	NB4	blood:	n/a	chr20:1447602-1447611 chr20:1447606-1447613
38	TBP	chr20:1448254-1448838	HepG2	liver:	n/a	n/a
39	CBX3	chr20:1448267-1448821	K562	blood:	n/a	n/a
40	CTCF	chr20:1448300-1448450	AG09319	gingival:	n/a	n/a
41	MAX	chr20:1446894-1448894	NB4	blood:	n/a	chr20:1447602-1447611 chr20:1447606-1447613
42	CEBPB	chr20:1448318-1448797	K562	blood:	n/a	n/a
43	POLR2A	chr20:1448158-1449116	K562	blood:	n/a	n/a
44	CHD2	chr20:1448324-1449089	K562	blood:	n/a	n/a
45	ELF1	chr20:1448018-1448702	K562	blood:	n/a	chr20:1448381-1448394
46	POLR2A	chr20:1445679-1448953	HepG2	liver:	n/a	n/a
47	POLR2A	chr20:1448305-1449451	K562	blood:	n/a	n/a
48	POLR2A	chr20:1446969-1449455	K562	blood:	n/a	n/a
49	RFX5	chr20:1448257-1448686	HepG2	liver:	n/a	n/a
50	TEAD4	chr20:1447943-1448857	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	chr20:1437321..1440209-chr20:1445376..1448458,3	MCF-7	breast:
4	chr20:1372232..1375944-chr20:1446656..1450761,3	MCF-7	breast:
5	chr20:1304611..1307577-chr20:1447050..1450049,5	K562	blood:
6	chr20:1372434..1374768-chr20:1446935..1449052,2	K562	blood:
7	chr20:1436244..1441221-chr20:1444525..1448562,4	MCF-7	breast:

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

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1543423	0.90[JPT][hapmap]
rs3795134	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3795135	0.95[JPT][hapmap]
rs6033860	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6033867	0.90[JPT][hapmap]
rs6033901	0.80[JPT][hapmap]
rs6033950	0.80[JPT][hapmap]
rs6042462	0.81[JPT][hapmap]
rs6042592	0.85[JPT][hapmap]
rs6074709	0.80[JPT][hapmap]
rs6074715	0.80[JPT][hapmap]
rs6079294	0.90[JPT][hapmap]
rs6079325	0.80[JPT][hapmap]
rs6079330	0.81[JPT][hapmap]
rs6079336	0.81[JPT][hapmap]
rs6079354	0.81[JPT][hapmap]
rs6079361	0.81[JPT][hapmap]
rs6110207	0.81[JPT][hapmap]
rs6110226	0.85[JPT][hapmap]
rs6135060	0.90[JPT][hapmap]
rs6135061	0.85[JPT][hapmap]
rs6135089	0.85[JPT][hapmap]
rs6135095	0.85[JPT][hapmap]
rs963867	0.90[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6135033	NSFL1C	cis	Whole Blood	GTEx
rs6135033	RP4-776F14.3	cis	Whole Blood	GTEx

Chromatin state (count:93 , 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	chr20:1447000-1448400	Active TSS	Rectal Smooth Muscle	rectum
4	chr20:1447600-1448400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:1447600-1448400	Enhancers	Esophagus	oesophagus
6	chr20:1447600-1448600	Enhancers	Lung	lung
7	chr20:1447600-1449000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr20:1447600-1449800	Weak transcription	Small Intestine	intestine
9	chr20:1447600-1450000	Weak transcription	Aorta	Aorta
10	chr20:1447800-1448400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr20:1447800-1448400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr20:1447800-1448400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr20:1447800-1448400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr20:1447800-1448400	Flanking Active TSS	Fetal Muscle Leg	muscle
15	chr20:1447800-1448400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
16	chr20:1447800-1448400	Flanking Active TSS	Pancreas	Pancrea
17	chr20:1447800-1448400	Flanking Active TSS	Thymus	Thymus
18	chr20:1447800-1448400	Flanking Active TSS	K562	blood
19	chr20:1447800-1448600	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr20:1447800-1448800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr20:1447800-1448800	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr20:1447800-1448800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr20:1447800-1448800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr20:1447800-1449000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr20:1447800-1449000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:1447800-1449000	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr20:1447800-1449000	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr20:1447800-1449000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr20:1447800-1449000	Flanking Bivalent TSS/Enh	HepG2	liver
30	chr20:1447800-1449400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr20:1448000-1448400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr20:1448000-1448400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr20:1448000-1448400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:1448000-1448400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:1448000-1448400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr20:1448000-1448400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr20:1448000-1448400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr20:1448000-1448400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:1448000-1448400	Enhancers	Brain Angular Gyrus	brain
40	chr20:1448000-1448400	Enhancers	A549	lung
41	chr20:1448000-1448600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr20:1448000-1448600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr20:1448000-1448800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr20:1448000-1449000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr20:1448000-1449400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr20:1448000-1449400	Weak transcription	NH-A	brain
47	chr20:1448000-1449600	Weak transcription	HSMM	muscle
48	chr20:1448000-1449600	Weak transcription	Osteobl	bone
49	chr20:1448000-1449800	Weak transcription	HSMMtube	muscle
50	chr20:1448000-1450200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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