Variant report

Variant	rs888821
Chromosome Location	chr5:80256909-80256910
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	MYBL2	chr5:80256502-80257316	HepG2	liver:	n/a	n/a
2	MAX	chr5:80255887-80257157	HepG2	liver:	n/a	chr5:80256133-80256142 chr5:80256372-80256382
3	CTCF	chr5:80256840-80256990	WI-38	lung:	n/a	n/a
4	RAD21	chr5:80256576-80257278	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr5:80255829-80257311	HepG2	liver:	n/a	chr5:80256134-80256143
6	CTCF	chr5:80256858-80256922	GM13976	blood:	n/a	n/a
7	YY1	chr5:80256310-80257172	H1-hESC	embryonic stem cell:	n/a	chr5:80256387-80256396 chr5:80256543-80256554 chr5:80256378-80256392
8	ZNF263	chr5:80255355-80257413	HEK293-T-REx	kidney:	n/a	chr5:80256995-80257016
9	MAX	chr5:80256024-80257019	A549	lung:	n/a	chr5:80256133-80256142 chr5:80256372-80256382
10	RAD21	chr5:80255862-80256959	IMR90	lung:	n/a	n/a
11	MAX	chr5:80255684-80257042	H1-hESC	embryonic stem cell:	n/a	chr5:80256133-80256142 chr5:80256372-80256382
12	MAX	chr5:80255669-80257408	HepG2	liver:	n/a	chr5:80256133-80256142 chr5:80256372-80256382
13	MYC	chr5:80256885-80256953	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTBP2	chr5:80255809-80257416	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr5:80256800-80256950	GM12866	blood:	n/a	n/a
16	SIN3A	chr5:80255732-80257235	H1-hESC	embryonic stem cell:	n/a	chr5:80255952-80255963
17	E2F6	chr5:80256015-80257065	H1-hESC	embryonic stem cell:	n/a	chr5:80256194-80256204 chr5:80256848-80256862 chr5:80256405-80256414 chr5:80256074-80256084
18	TAF1	chr5:80255847-80257135	HepG2	liver:	n/a	n/a
19	POLR2A	chr5:80255661-80257284	HepG2	liver:	n/a	n/a
20	CREB1	chr5:80255584-80257085	HepG2	liver:	n/a	n/a
21	RAD21	chr5:80256266-80257167	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F6	chr5:80256260-80256944	A549	lung:	n/a	chr5:80256848-80256862 chr5:80256405-80256414
23	MAX	chr5:80255663-80257435	HepG2	liver:	n/a	chr5:80256133-80256142 chr5:80256372-80256382
24	MAX	chr5:80256299-80257041	H1-hESC	embryonic stem cell:	n/a	chr5:80256372-80256382
25	RCOR1	chr5:80256699-80256996	HepG2	liver:	n/a	n/a
26	E2F6	chr5:80256271-80256966	H1-hESC	embryonic stem cell:	n/a	chr5:80256848-80256862 chr5:80256405-80256414
27	POLR2A	chr5:80255440-80257187	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000251450	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10942936	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942937	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520354	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1900148	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32984	1.00[ASN][1000 genomes]
rs34134330	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550784	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34586090	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67175576	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs960990	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3322696	chr5:80255021-80257569	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3330937	chr5:80255346-80257994	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv15582	chr5:80255351-80256937	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3359411	chr5:80255421-80257969	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1822121	chr5:80255984-80257109	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80255400-80257400	Active TSS	Colon Smooth Muscle	Colon
2	chr5:80255600-80257000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:80255600-80257000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:80255600-80257000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr5:80255600-80257000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
6	chr5:80255600-80257000	Bivalent/Poised TSS	HSMM	muscle
7	chr5:80255600-80257200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:80255600-80257200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:80255600-80257400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:80255600-80257400	Bivalent/Poised TSS	Osteobl	bone
11	chr5:80255600-80258000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
12	chr5:80255600-80258000	Active TSS	Ovary	ovary
13	chr5:80255800-80257000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:80255800-80257000	Active TSS	Aorta	Aorta
15	chr5:80255800-80257000	Bivalent/Poised TSS	A549	lung
16	chr5:80255800-80257000	Flanking Bivalent TSS/Enh	HMEC	breast
17	chr5:80255800-80257000	Bivalent/Poised TSS	HSMMtube	muscle
18	chr5:80255800-80257000	Bivalent/Poised TSS	NH-A	brain
19	chr5:80255800-80257200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:80255800-80257400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr5:80255800-80257400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
22	chr5:80255800-80257600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr5:80255800-80258000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr5:80255800-80258000	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr5:80255800-80258000	Active TSS	Brain Anterior Caudate	brain
26	chr5:80255800-80258000	Bivalent/Poised TSS	Psoas Muscle	Psoas
27	chr5:80255800-80258200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr5:80255800-80258200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr5:80255800-80258200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr5:80255800-80258200	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr5:80255800-80259000	Active TSS	NHLF	lung
32	chr5:80255800-80259600	Active TSS	Brain Substantia Nigra	brain
33	chr5:80255800-80261000	Active TSS	Right Atrium	heart
34	chr5:80255800-80261200	Active TSS	Brain Cingulate Gyrus	brain
35	chr5:80255800-80261600	Active TSS	Brain Angular Gyrus	brain
36	chr5:80256000-80257000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:80256000-80257000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr5:80256000-80257000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:80256000-80257000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:80256000-80257000	Active TSS	Primary B cells from cord blood	blood
41	chr5:80256000-80257000	Active TSS	Primary T cells from cord blood	blood
42	chr5:80256000-80257000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:80256000-80257000	Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr5:80256000-80257000	Bivalent/Poised TSS	Fetal Lung	lung
45	chr5:80256000-80257200	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr5:80256000-80257200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
47	chr5:80256000-80257400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
48	chr5:80256000-80257800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:80256000-80257800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:80256000-80257800	Bivalent/Poised TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links