Variant report

Variant	rs72775801
Chromosome Location	chr5:75840515-75840516
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	RAD21	chr5:75840111-75840586	ECC-1	luminal epithelium:	n/a	chr5:75840321-75840340
2	CTCF	chr5:75840420-75840570	HFF	foreskin:	n/a	n/a
3	POLR2A	chr5:75838483-75840557	PBDE	blood:	n/a	n/a
4	ARID3A	chr5:75840098-75840519	HepG2	liver:	n/a	n/a
5	SMC3	chr5:75840124-75840515	K562	blood:	n/a	chr5:75840325-75840339
6	RAD21	chr5:75840077-75840569	A549	lung:	n/a	chr5:75840321-75840340
7	CTCF	chr5:75840108-75840531	T-47D	breast:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
8	RAD21	chr5:75840128-75840600	MCF-7	breast:	n/a	chr5:75840321-75840340
9	SMC3	chr5:75840113-75840534	HepG2	liver:	n/a	chr5:75840325-75840339
10	STAT1	chr5:75840358-75840532	GM12878	blood:	n/a	n/a
11	SMC3	chr5:75839628-75840700	SK-N-SH	brain:	n/a	chr5:75840325-75840339
12	RAD21	chr5:75839999-75840617	MCF-7	breast:	n/a	chr5:75840321-75840340
13	CTCF	chr5:75840029-75840689	HCT-116	colon:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
14	CTCF	chr5:75840109-75840561	MCF-7	breast:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
15	RAD21	chr5:75840107-75840539	H1-hESC	embryonic stem cell:	n/a	chr5:75840321-75840340
16	RAD21	chr5:75839690-75840758	SK-N-SH	brain:	n/a	chr5:75840321-75840340
17	SMC3	chr5:75840155-75840567	GM12878	blood:	n/a	chr5:75840325-75840339
18	CTCF	chr5:75840205-75840614	HCT-116	colon:	n/a	chr5:75840318-75840339
19	CTCF	chr5:75839813-75840696	SK-N-SH	brain:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
20	RAD21	chr5:75840088-75840519	SK-N-SH_RA	brain:	n/a	chr5:75840321-75840340
21	RAD21	chr5:75840068-75840541	HepG2	liver:	n/a	chr5:75840321-75840340
22	CTCF	chr5:75840143-75840559	MCF-7	breast:	n/a	chr5:75840318-75840339
23	RAD21	chr5:75840091-75840587	A549	lung:	n/a	chr5:75840321-75840340
24	CTCF	chr5:75839606-75840679	A549	lung:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
25	RAD21	chr5:75840131-75840516	GM12878	blood:	n/a	chr5:75840321-75840340
26	RAD21	chr5:75840029-75840603	HCT-116	colon:	n/a	chr5:75840321-75840340
27	CTCF	chr5:75840116-75840536	K562	blood:	n/a	chr5:75840318-75840339
28	RAD21	chr5:75840031-75840637	HCT-116	colon:	n/a	chr5:75840321-75840340
29	CTCF	chr5:75840110-75840539	GM12878	blood:	n/a	chr5:75840111-75840120 chr5:75840318-75840339
30	RAD21	chr5:75839986-75840582	HepG2	liver:	n/a	chr5:75840321-75840340
31	RAD21	chr5:75839893-75840565	H1-hESC	embryonic stem cell:	n/a	chr5:75840321-75840340
32	RUNX3	chr5:75840101-75840548	GM12878	blood:	n/a	n/a
33	ARID3A	chr5:75840176-75840537	K562	blood:	n/a	n/a
34	RAD21	chr5:75840008-75840534	SK-N-SH_RA	brain:	n/a	chr5:75840321-75840340
35	CTCF	chr5:75840123-75840534	H1-hESC	embryonic stem cell:	n/a	chr5:75840318-75840339

No.	Distal block	Cell Line	Cell type
1	chr5:75628819..75631136-chr5:75840007..75842103,2	K562	blood:
2	chr5:75633886..75634436-chr5:75839825..75840735,2	K562	blood:
3	chr5:75698517..75699563-chr5:75839811..75840781,6	MCF-7	breast:
4	chr5:75633417..75634381-chr5:75839891..75840630,3	MCF-7	breast:
5	chr5:75633462..75634419-chr5:75839412..75840924,7	MCF-7	breast:

Variant related genes	Relation type
IQGAP2	TF binding region
ENSG00000145703	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16873461	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16873476	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16873483	0.84[EUR][1000 genomes]
rs3913473	0.88[EUR][1000 genomes]
rs3913474	0.90[EUR][1000 genomes]
rs3913475	0.90[EUR][1000 genomes]
rs4704327	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4704328	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704334	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4704335	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4704337	0.85[EUR][1000 genomes]
rs58542602	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361989	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62361990	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62361991	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62361992	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62361993	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62361994	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62361997	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62362011	0.83[EUR][1000 genomes]
rs62362012	0.84[EUR][1000 genomes]
rs62362014	0.83[EUR][1000 genomes]
rs62362016	0.86[EUR][1000 genomes]
rs72777503	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS 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	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
2	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:75837400-75840600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:75837400-75842800	Enhancers	Liver	Liver
5	chr5:75837800-75840600	Enhancers	Fetal Lung	lung
6	chr5:75837800-75841200	Enhancers	Placenta	Placenta
7	chr5:75838000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:75838200-75840600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr5:75838200-75841400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr5:75838400-75840600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr5:75838400-75840600	Enhancers	Fetal Kidney	kidney
12	chr5:75838600-75840600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:75839000-75840600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:75839000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:75839000-75841600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr5:75839200-75840600	Enhancers	Pancreas	Pancrea
17	chr5:75839200-75840800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr5:75839200-75841400	Enhancers	Fetal Intestine Small	intestine
19	chr5:75839400-75840600	Enhancers	Primary B cells from cord blood	blood
20	chr5:75839400-75840600	Enhancers	Primary T cells from cord blood	blood
21	chr5:75839400-75840600	Enhancers	K562	blood
22	chr5:75839400-75840600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr5:75839400-75842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:75839400-75842400	Weak transcription	Adipose Nuclei	Adipose
25	chr5:75839400-75842600	Weak transcription	Thymus	Thymus
26	chr5:75839600-75845400	Enhancers	HepG2	liver
27	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr5:75839800-75840600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr5:75839800-75840600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr5:75839800-75842200	Enhancers	GM12878-XiMat	blood
32	chr5:75840000-75840600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:75840000-75841200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr5:75840000-75841600	Enhancers	Duodenum Mucosa	Duodenum
35	chr5:75840000-75842400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:75840000-75842600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr5:75840200-75842200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:75840200-75842400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:75840200-75842400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:75840200-75842400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:75840200-75842400	Weak transcription	Colonic Mucosa	Colon
42	chr5:75840200-75842400	Weak transcription	Fetal Stomach	stomach
43	chr5:75840200-75842400	Weak transcription	Gastric	stomach
44	chr5:75840200-75842400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:75840200-75842400	Weak transcription	Small Intestine	intestine
46	chr5:75840200-75842600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr5:75840200-75842800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:75840200-75842800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr5:75840200-75842800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr5:75840200-75842800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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