Variant report

Variant	rs6131543
Chromosome Location	chr20:1451126-1451127
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	MAX	chr20:1450808-1451138	H1-hESC	embryonic stem cell:	n/a	chr20:1451011-1451021
2	FOXA2	chr20:1450652-1451198	A549	lung:	n/a	n/a
3	RCOR1	chr20:1450181-1452208	IMR90	lung:	n/a	n/a
4	MAX	chr20:1450478-1451216	A549	lung:	n/a	chr20:1451011-1451021
5	NFATC1	chr20:1450804-1451159	GM12878	blood:	n/a	n/a
6	RELA	chr20:1450708-1451168	GM19193	blood:	n/a	n/a
7	STAT3	chr20:1450598-1451230	MCF10A-Er-Src	breast:	n/a	n/a
8	SMC3	chr20:1450543-1451240	SK-N-SH	brain:	n/a	chr20:1450872-1450886
9	CTCF	chr20:1450438-1451158	HCT-116	colon:	n/a	chr20:1450872-1450885 chr20:1450865-1450886 chr20:1450871-1450887 chr20:1450870-1450888
10	POLR2A	chr20:1450470-1451324	IMR90	lung:	n/a	n/a
11	POLR2A	chr20:1450582-1451162	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr20:1450589-1451264	MCF10A-Er-Src	breast:	n/a	chr20:1451011-1451021
13	YY1	chr20:1450678-1451127	GM12878	blood:	n/a	n/a
14	BCL3	chr20:1450604-1451234	A549	lung:	n/a	n/a
15	TBP	chr20:1450732-1451145	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr20:1450673-1451226	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr20:1450527-1451130	HepG2	liver:	n/a	chr20:1450868-1450887 chr20:1450872-1450886
18	POLR2A	chr20:1450448-1451329	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr20:1450423-1451138	SK-N-SH	brain:	n/a	n/a
20	STAT3	chr20:1450607-1451188	MCF10A-Er-Src	breast:	n/a	n/a
21	GATA3	chr20:1450303-1451271	A549	lung:	n/a	n/a
22	MYBL2	chr20:1450486-1451255	HepG2	liver:	n/a	n/a
23	SP1	chr20:1450419-1451273	A549	lung:	n/a	n/a
24	POLR2A	chr20:1450532-1451130	PANC-1	pancreas:	n/a	n/a
25	CTCF	chr20:1450220-1451246	SK-N-SH	brain:	n/a	chr20:1450872-1450885 chr20:1450389-1450402 chr20:1450865-1450886 chr20:1450871-1450887 chr20:1450870-1450888
26	RAD21	chr20:1450420-1451167	SK-N-SH	brain:	n/a	chr20:1450868-1450887 chr20:1450872-1450886
27	MAFK	chr20:1450526-1451223	IMR90	lung:	n/a	chr20:1450701-1450716 chr20:1450593-1450603
28	JUN	chr20:1450460-1451170	K562	blood:	n/a	n/a
29	CEBPB	chr20:1450542-1451318	IMR90	lung:	n/a	n/a
30	E2F4	chr20:1450504-1451183	MCF10A-Er-Src	breast:	n/a	n/a
31	TCF12	chr20:1450408-1451192	A549	lung:	n/a	n/a
32	RAD21	chr20:1450575-1451162	A549	lung:	n/a	chr20:1450868-1450887 chr20:1450872-1450886
33	BCL11A	chr20:1450806-1451141	GM12878	blood:	n/a	n/a
34	RAD21	chr20:1450503-1451227	HCT-116	colon:	n/a	chr20:1450868-1450887 chr20:1450872-1450886
35	YY1	chr20:1450696-1451162	A549	lung:	n/a	n/a
36	RELA	chr20:1450766-1451160	GM19099	blood:	n/a	n/a
37	RAD21	chr20:1450572-1451152	ECC-1	luminal epithelium:	n/a	chr20:1450868-1450887 chr20:1450872-1450886
38	CTCF	chr20:1450602-1451160	MCF-7	breast:	n/a	chr20:1450872-1450885 chr20:1450865-1450886 chr20:1450871-1450887 chr20:1450870-1450888
39	POU2F2	chr20:1450684-1451231	GM12878	blood:	n/a	n/a
40	BCL3	chr20:1450504-1451168	A549	lung:	n/a	n/a
41	FOS	chr20:1450502-1451252	MCF10A-Er-Src	breast:	n/a	n/a
42	CHD1	chr20:1450304-1451859	IMR90	lung:	n/a	n/a
43	FOS	chr20:1450455-1451252	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr20:1450421-1451141	IMR90	lung:	n/a	chr20:1450872-1450885 chr20:1450865-1450886 chr20:1450871-1450887 chr20:1450870-1450888
45	FOS	chr20:1450522-1451216	MCF10A-Er-Src	breast:	n/a	n/a
46	BHLHE40	chr20:1450766-1451157	GM12878	blood:	n/a	n/a
47	STAT3	chr20:1450578-1451191	MCF10A-Er-Src	breast:	n/a	n/a
48	RAD21	chr20:1450546-1451211	HCT-116	colon:	n/a	chr20:1450868-1450887 chr20:1450872-1450886
49	MYBL2	chr20:1450402-1451142	HepG2	liver:	n/a	n/a
50	RAD21	chr20:1450598-1451146	H1-hESC	embryonic stem cell:	n/a	chr20:1450868-1450887 chr20:1450872-1450886

No.	Distal block	Cell Line	Cell type
1	chr20:1447071..1448806-chr20:1450889..1452867,2	MCF-7	breast:
2	chr20:1405279..1407726-chr20:1449432..1451429,2	K562	blood:
3	chr20:1449411..1451368-chr20:1451842..1453963,2	K562	blood:
4	chr20:1450508..1451201-chr20:1483798..1484780,3	MCF-7	breast:
5	chr20:1450041..1452334-chr20:1456617..1458188,2	K562	blood:
6	chr20:1205294..1207984-chr20:1450527..1452708,2	MCF-7	breast:
7	chr20:1397834..1399758-chr20:1450418..1453215,2	K562	blood:
8	chr20:1420460..1421270-chr20:1450721..1451369,3	MCF-7	breast:

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000088833	Chromatin interaction
ENSG00000244588	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1543423	0.98[ASN][1000 genomes]
rs1884387	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143832	0.83[ASN][1000 genomes]
rs2873565	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033860	0.87[ASN][1000 genomes]
rs6033867	0.98[ASN][1000 genomes]
rs6033901	0.91[ASN][1000 genomes]
rs6033910	0.92[ASN][1000 genomes]
rs6033950	0.82[ASN][1000 genomes]
rs6042499	0.96[ASN][1000 genomes]
rs6042500	0.98[ASN][1000 genomes]
rs6042592	0.92[ASN][1000 genomes]
rs6042602	0.92[ASN][1000 genomes]
rs6042611	0.90[ASN][1000 genomes]
rs6042650	0.87[ASN][1000 genomes]
rs6074709	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074715	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6074718	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6079277	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079288	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079289	0.97[ASN][1000 genomes]
rs6079294	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079302	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079317	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6079330	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079336	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079354	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079361	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079362	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079376	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6105233	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6105234	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6105240	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6110169	0.95[ASN][1000 genomes]
rs6110207	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6110215	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6110226	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6110228	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6110253	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6110261	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6110262	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6131553	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6131559	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6135048	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135050	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135060	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6135061	0.97[ASN][1000 genomes]
rs6135062	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6135063	0.97[ASN][1000 genomes]
rs6135064	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6135068	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135069	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135080	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135089	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135095	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135105	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7270432	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963867	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6131543	SIRPB2	cis	lung	GTEx
rs6131543	SIRPB2	cis	Whole Blood	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1448200-1451200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:1448200-1451600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:1448200-1451600	Enhancers	Placenta	Placenta
4	chr20:1448200-1451600	Enhancers	Stomach Mucosa	stomach
5	chr20:1448200-1452200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr20:1448200-1455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:1448200-1457400	Weak transcription	Spleen	Spleen
8	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:1448400-1452200	Weak transcription	Esophagus	oesophagus
10	chr20:1448600-1451400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr20:1448800-1452000	Enhancers	Duodenum Mucosa	Duodenum
12	chr20:1448800-1452000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr20:1449000-1451400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr20:1449000-1453600	Enhancers	Primary B cells from cord blood	blood
15	chr20:1449000-1454800	Enhancers	Fetal Intestine Small	intestine
16	chr20:1449400-1454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:1449400-1454200	Enhancers	K562	blood
18	chr20:1449600-1451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:1449600-1451800	Enhancers	HMEC	breast
20	chr20:1449600-1452000	Enhancers	HUVEC	blood vessel
21	chr20:1449600-1452800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr20:1449800-1451600	Enhancers	NHDF-Ad	bronchial
23	chr20:1449800-1452000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:1449800-1453800	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr20:1450000-1451200	Flanking Active TSS	HepG2	liver
26	chr20:1450000-1451600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr20:1450000-1451800	Enhancers	Hela-S3	cervix
28	chr20:1450000-1453000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
29	chr20:1450200-1451200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr20:1450200-1451200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr20:1450200-1451800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr20:1450200-1452000	Enhancers	NHEK	skin
33	chr20:1450400-1451200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr20:1450400-1451200	Enhancers	Primary B cells from peripheral blood	blood
35	chr20:1450400-1451200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr20:1450400-1451200	Weak transcription	Small Intestine	intestine
37	chr20:1450400-1451200	Active TSS	A549	lung
38	chr20:1450400-1451400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:1450400-1451400	Weak transcription	Gastric	stomach
40	chr20:1450400-1451400	Weak transcription	HSMMtube	muscle
41	chr20:1450400-1451600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr20:1450400-1453800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr20:1450400-1459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr20:1450400-1459000	Weak transcription	Lung	lung
45	chr20:1450600-1451200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr20:1450600-1451200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr20:1450600-1451400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:1450600-1451400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr20:1450600-1451400	Enhancers	GM12878-XiMat	blood
50	chr20:1450600-1451400	Active TSS	NH-A	brain

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