Variant report

Variant	rs321633
Chromosome Location	chr4:48018529-48018530
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	chr4:48018318-48018969	HepG2	liver:	n/a	n/a
2	MYC	chr4:48018345-48018992	K562	blood:	n/a	n/a
3	CTCF	chr4:48018374-48018575	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr4:48018520-48018670	A549	lung:	n/a	n/a
5	POLR2A	chr4:48018414-48019331	GM18505	blood:	n/a	n/a
6	MAX	chr4:48018362-48018562	A549	lung:	n/a	n/a
7	CTCF	chr4:48018380-48018530	GM12869	blood:	n/a	n/a
8	NR2F2	chr4:48018230-48019080	MCF-7	breast:	n/a	n/a
9	MAZ	chr4:48018347-48019012	K562	blood:	n/a	n/a
10	POLR2A	chr4:48018435-48018980	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr4:48018237-48018639	K562	blood:	n/a	n/a
12	POLR2A	chr4:48018466-48018927	GM12891	blood:	n/a	n/a
13	POLR2A	chr4:48018512-48018944	HUVEC	blood vessel:	n/a	n/a
14	E2F6	chr4:48018272-48019360	H1-hESC	embryonic stem cell:	n/a	chr4:48018748-48018762 chr4:48018778-48018787 chr4:48018739-48018748
15	CTCF	chr4:48018380-48018530	NHEK	skin:	n/a	n/a
16	TBL1XR1	chr4:48018375-48018725	GM12878	blood:	n/a	n/a
17	PAX5	chr4:48018381-48018949	GM12892	blood:	n/a	n/a
18	TAF1	chr4:48018344-48018958	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr4:48018400-48018550	AG04450	lung:	n/a	n/a
20	RAD21	chr4:48018175-48018657	HepG2	liver:	n/a	chr4:48018447-48018466
21	STAT5A	chr4:48018321-48018627	GM12878	blood:	n/a	chr4:48018481-48018501
22	RAD21	chr4:48018163-48018609	H1-hESC	embryonic stem cell:	n/a	chr4:48018447-48018466
23	CTCF	chr4:48018400-48018550	GM12878	blood:	n/a	n/a
24	MYC	chr4:48018503-48019580	MCF10A-Er-Src	breast:	n/a	chr4:48019432-48019441 chr4:48019176-48019183
25	RAD21	chr4:48018300-48018591	K562	blood:	n/a	chr4:48018447-48018466
26	RAD21	chr4:48018175-48018657	ECC-1	luminal epithelium:	n/a	chr4:48018447-48018466
27	CTCF	chr4:48018380-48018530	GM12870	blood:	n/a	n/a
28	CEBPD	chr4:48018376-48018957	HepG2	liver:	n/a	n/a
29	RFX5	chr4:48018356-48019298	Hela-S3	cervix:	n/a	n/a
30	TCF12	chr4:48018136-48019597	ECC-1	luminal epithelium:	n/a	chr4:48018588-48018598
31	CTCF	chr4:48018335-48018548	GM10266	blood:	n/a	n/a
32	CTCF	chr4:48018348-48018562	HUVEC	blood vessel:	n/a	n/a
33	SETDB1	chr4:48018229-48018666	U2OS	brain:	n/a	n/a
34	POLR2A	chr4:48018308-48018991	GM12878	blood:	n/a	n/a
35	BCLAF1	chr4:48018183-48019163	GM12878	blood:	n/a	chr4:48018766-48018779 chr4:48018770-48018783
36	TFAP2C	chr4:48018288-48019589	Hela-S3	cervix:	n/a	n/a
37	TBP	chr4:48018507-48018947	K562	blood:	n/a	n/a
38	CTBP2	chr4:48018238-48019635	H1-hESC	embryonic stem cell:	n/a	n/a
39	CHD2	chr4:48018411-48018918	HepG2	liver:	n/a	n/a
40	MAZ	chr4:48018275-48019179	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr4:48018400-48018550	AG04449	skin:	n/a	n/a
42	CTCF	chr4:48018180-48018608	HepG2	liver:	n/a	n/a
43	YY1	chr4:48018420-48019063	HepG2	liver:	n/a	chr4:48018730-48018744 chr4:48018739-48018748 chr4:48018770-48018781
44	POLR2A	chr4:48018332-48018941	H1-hESC	embryonic stem cell:	n/a	n/a
45	STAT5A	chr4:48018104-48018656	GM12878	blood:	n/a	chr4:48018112-48018119 chr4:48018481-48018501 chr4:48018105-48018119
46	POLR2A	chr4:48018461-48019264	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr4:48018246-48018590	T-47D	breast:	n/a	n/a
48	CTCF	chr4:48018400-48018550	WI-38	lung:	n/a	n/a
49	CTCF	chr4:48018126-48018765	K562	blood:	n/a	n/a
50	CTCF	chr4:48018380-48018530	GM12874	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:47915045..47916605-chr4:48017433..48018940,2	MCF-7	breast:
2	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:
3	chr4:48018226..48018849-chr5:157285675..157286547,2	HCT-116	colon:

Variant related genes	Relation type
NIPAL1	TF binding region
CNGA1	TF binding region
ENSG00000170448	Chromatin interaction
ENSG00000113282	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10002500	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap]
rs10517204	0.89[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10805163	0.89[CEU][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10938520	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11733288	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12645245	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371732	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1396051	0.89[CEU][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1507913	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1507914	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs178650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1837518	0.91[ASN][1000 genomes]
rs1866688	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap]
rs188901	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1899060	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs224800	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2581493	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2661513	0.83[JPT][hapmap]
rs28578328	0.81[EUR][1000 genomes]
rs28642966	0.86[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap]
rs28699496	0.84[ASN][1000 genomes]
rs3113881	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113882	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs321621	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321642	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs321644	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs321646	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3950558	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4694880	0.89[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4695326	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447603	0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap]
rs6850603	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7685636	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs321633	NFXL1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48017400-48019200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48017400-48020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:48017600-48019000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr4:48017600-48019000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr4:48017600-48019200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:48017600-48020600	Active TSS	Rectal Smooth Muscle	rectum
7	chr4:48017800-48018600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr4:48017800-48018800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:48017800-48019000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:48017800-48019200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:48017800-48019600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:48017800-48019800	Active TSS	Esophagus	oesophagus
13	chr4:48017800-48019800	Active TSS	Fetal Kidney	kidney
14	chr4:48018000-48018600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr4:48018000-48018600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:48018000-48018600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr4:48018000-48018600	Active TSS	HepG2	liver
18	chr4:48018000-48018600	Flanking Active TSS	HMEC	breast
19	chr4:48018000-48018800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:48018000-48018800	Active TSS	Fetal Intestine Small	intestine
21	chr4:48018000-48019000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:48018000-48019000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:48018000-48019400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr4:48018000-48019400	Active TSS	Fetal Heart	heart
25	chr4:48018000-48019400	Active TSS	A549	lung
26	chr4:48018000-48019600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:48018000-48019600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:48018000-48019600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:48018000-48019600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr4:48018000-48019600	Active TSS	Brain Substantia Nigra	brain
32	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr4:48018000-48019600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr4:48018000-48019800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:48018000-48019800	Active TSS	NH-A	brain
36	chr4:48018000-48020000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:48018000-48020400	Active TSS	Duodenum Mucosa	Duodenum
38	chr4:48018000-48020600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:48018200-48018600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:48018200-48018600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
43	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr4:48018200-48018600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:48018200-48018600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr4:48018200-48018600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:48018200-48018600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin

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