Variant report

Variant	rs782599
Chromosome Location	chr2:55847423-55847424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:143)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:143 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:55847400-55847550	NB4	blood:	n/a	n/a
2	RAD21	chr2:55847363-55847559	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr2:55847411-55847582	GM10266	blood:	n/a	n/a
4	POLR2A	chr2:55847151-55847610	HepG2	liver:	n/a	n/a
5	CTCF	chr2:55847420-55847570	AG09309	skin:	n/a	n/a
6	MXI1	chr2:55847299-55847696	HepG2	liver:	n/a	n/a
7	RAD21	chr2:55847374-55847679	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr2:55847417-55847582	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr2:55847420-55847570	GM12871	blood:	n/a	n/a
10	RCOR1	chr2:55847337-55847658	K562	blood:	n/a	n/a
11	CTCF	chr2:55847402-55847605	GM13977	blood:	n/a	n/a
12	CTCF	chr2:55847420-55847569	LNCaP	prostate:	n/a	n/a
13	CTCF	chr2:55847420-55847570	GM12866	blood:	n/a	n/a
14	RFX5	chr2:55847385-55847511	HepG2	liver:	n/a	n/a
15	CTCF	chr2:55847420-55847570	WI-38	lung:	n/a	n/a
16	CTCF	chr2:55847273-55847702	GM12878	blood:	n/a	n/a
17	CTCF	chr2:55847400-55847550	HCFaa	heart:	n/a	n/a
18	CTCF	chr2:55847387-55847605	GM12892	blood:	n/a	n/a
19	CTCF	chr2:55847386-55847601	GM19239	blood:	n/a	n/a
20	CTCF	chr2:55847394-55847610	GM10248	blood:	n/a	n/a
21	CTCF	chr2:55847420-55847570	HepG2	liver:	n/a	n/a
22	CTCF	chr2:55847400-55847550	HMF	breast:	n/a	n/a
23	CTCF	chr2:55847400-55847550	AoAF	blood vessel:	n/a	n/a
24	CTCF	chr2:55847400-55847550	GM12866	blood:	n/a	n/a
25	CTCF	chr2:55847380-55847530	HRE	kidney:	n/a	n/a
26	CTCF	chr2:55847407-55847622	HepG2	liver:	n/a	n/a
27	RAD21	chr2:55847352-55847641	Hela-S3	cervix:	n/a	n/a
28	MYC	chr2:55847347-55847615	MCF10A-Er-Src	breast:	n/a	n/a
29	CTCF	chr2:55847389-55847621	Medullo	brain:	n/a	n/a
30	POLR2A	chr2:55847375-55847459	MCF10A-Er-Src	breast:	n/a	n/a
31	CTCF	chr2:55847329-55847662	IMR90	lung:	n/a	n/a
32	PBX3	chr2:55847321-55847736	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr2:55847312-55847699	K562	blood:	n/a	n/a
34	ZNF143	chr2:55847306-55847684	H1-hESC	embryonic stem cell:	n/a	n/a
35	PAX5	chr2:55847352-55847609	GM12878	blood:	n/a	n/a
36	RAD21	chr2:55847332-55847615	HepG2	liver:	n/a	n/a
37	CTCF	chr2:55847420-55847570	HMF	breast:	n/a	n/a
38	ZMIZ1	chr2:55847318-55847489	K562	blood:	n/a	n/a
39	CTCF	chr2:55847380-55847530	GM12801	blood:	n/a	n/a
40	RAD21	chr2:55847381-55847547	K562	blood:	n/a	n/a
41	CTCF	chr2:55847395-55847610	Fibrobl	skin:	n/a	n/a
42	CTCF	chr2:55847420-55847570	AG04449	skin:	n/a	n/a
43	CTCF	chr2:55847395-55847611	MCF-7	breast:	n/a	n/a
44	SMC3	chr2:55847336-55847631	K562	blood:	n/a	n/a
45	CTCF	chr2:55847386-55847587	MCF-7	breast:	n/a	n/a
46	CTCF	chr2:55847388-55847600	GM19240	blood:	n/a	n/a
47	POLR2A	chr2:55847387-55847855	HepG2	liver:	n/a	n/a
48	FOXA2	chr2:55847349-55847616	HepG2	liver:	n/a	n/a
49	CTCF	chr2:55847287-55847678	A549	lung:	n/a	n/a
50	YY1	chr2:55847396-55847575	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55846036..55847829-chr2:55873560..55876152,3	K562	blood:
2	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
3	chr2:55845275..55847536-chr2:55874365..55876152,2	K562	blood:
4	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000115355	Chromatin interaction
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10165864	0.92[CEU][hapmap]
rs10454749	0.80[AMR][1000 genomes]
rs10460508	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10496050	0.85[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1058582	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1084522	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1084525	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11125581	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12329050	0.87[YRI][hapmap]
rs17278044	0.86[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17369191	0.86[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17798852	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1823893	0.86[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975484	0.86[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975487	0.82[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs2054728	0.83[AFR][1000 genomes]
rs2586947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586950	0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2586954	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs2586968	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586969	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2586970	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2627759	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627765	1.00[YRI][hapmap]
rs2627773	1.00[YRI][hapmap]
rs2627775	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2627776	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627777	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2627780	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2627782	0.97[AFR][1000 genomes]
rs35504023	0.85[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762513	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4290693	0.85[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4312532	0.95[YRI][hapmap]
rs4672052	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs4672054	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4672055	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672056	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55761024	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58003472	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165173	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62165181	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62165182	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165183	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165184	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165196	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62165197	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165200	0.93[AFR][1000 genomes]
rs6545506	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6739513	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6744213	0.83[AFR][1000 genomes]
rs706548	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7582278	0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7594279	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7596377	0.87[YRI][hapmap]
rs7598650	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782566	0.80[AFR][1000 genomes]
rs782567	0.81[AFR][1000 genomes]
rs782568	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782572	0.87[YRI][hapmap]
rs782573	0.87[YRI][hapmap]
rs782584	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs782586	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782587	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782588	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782590	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782594	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782595	0.86[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782602	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782606	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs782613	0.84[AFR][1000 genomes]
rs782629	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs782630	1.00[YRI][hapmap]
rs782632	1.00[YRI][hapmap]
rs782634	1.00[YRI][hapmap]
rs782637	1.00[YRI][hapmap]
rs782649	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782650	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782652	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs809732	0.87[YRI][hapmap]
rs935177	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9917139	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs782599	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55842800-55847800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:55846000-55847600	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr2:55846200-55847600	Enhancers	Placenta	Placenta
4	chr2:55846200-55847800	Flanking Active TSS	Hela-S3	cervix
5	chr2:55846400-55848000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:55846400-55848000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
8	chr2:55846600-55847600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:55846600-55847600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:55846600-55847600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:55846600-55847600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr2:55846600-55847600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:55846600-55847600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr2:55846600-55847600	Enhancers	Fetal Brain Male	brain
15	chr2:55846600-55847600	Enhancers	Fetal Lung	lung
16	chr2:55846600-55847600	Enhancers	Fetal Muscle Leg	muscle
17	chr2:55846600-55847600	Enhancers	Gastric	stomach
18	chr2:55846600-55847600	Enhancers	Left Ventricle	heart
19	chr2:55846600-55847600	Enhancers	Right Atrium	heart
20	chr2:55846600-55847600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr2:55846600-55847600	Enhancers	Spleen	Spleen
22	chr2:55846600-55847800	Enhancers	Primary hematopoietic stem cells	blood
23	chr2:55846600-55847800	Enhancers	Brain Substantia Nigra	brain
24	chr2:55846600-55847800	Genic enhancers	Fetal Stomach	stomach
25	chr2:55846600-55847800	Enhancers	Right Ventricle	heart
26	chr2:55846600-55847800	Enhancers	HUVEC	blood vessel
27	chr2:55846600-55847800	Enhancers	NH-A	brain
28	chr2:55846600-55847800	Enhancers	NHEK	skin
29	chr2:55846600-55848000	Enhancers	Small Intestine	intestine
30	chr2:55846600-55848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:55846600-55848600	Weak transcription	Esophagus	oesophagus
32	chr2:55846600-55848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:55846600-55849000	Enhancers	Colon Smooth Muscle	Colon
34	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
42	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:55846800-55847600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:55846800-55847600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:55846800-55847600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:55846800-55847600	Enhancers	Brain Anterior Caudate	brain
48	chr2:55846800-55847600	Enhancers	Colonic Mucosa	Colon
49	chr2:55846800-55847600	Enhancers	Fetal Thymus	thymus
50	chr2:55846800-55847600	Enhancers	Psoas Muscle	Psoas

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