Variant report

Variant	rs30192
Chromosome Location	chr5:75370597-75370598
allele	G/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	CTCF	chr5:75370384-75370650	GM12878	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
2	CTCF	chr5:75370326-75370718	GM12878	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
3	CTCF	chr5:75370410-75370624	GM19240	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
4	CTCF	chr5:75370398-75370612	HUVEC	blood vessel:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
5	RAD21	chr5:75370362-75370728	SK-N-SH_RA	brain:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
6	CTCF	chr5:75370296-75370727	H1-hESC	embryonic stem cell:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
7	RAD21	chr5:75370381-75370599	Hela-S3	cervix:	n/a	chr5:75370511-75370530
8	RAD21	chr5:75370347-75370708	GM12878	blood:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
9	RAD21	chr5:75370312-75370734	SK-N-SH_RA	brain:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
10	CTCF	chr5:75370385-75370650	MCF-7	breast:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
11	CTCF	chr5:75370423-75370607	Gliobla	brain:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
12	SMC3	chr5:75370380-75370653	HepG2	liver:	n/a	chr5:75370512-75370519
13	RAD21	chr5:75370373-75370768	HCT-116	colon:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
14	CTCF	chr5:75370294-75370817	MCF-7	breast:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
15	CTCF	chr5:75370331-75370646	K562	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
16	RAD21	chr5:75370324-75370636	GM12878	blood:	n/a	chr5:75370511-75370530
17	CTCF	chr5:75370426-75370626	GM19238	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
18	CTCF	chr5:75370418-75370612	HepG2	liver:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
19	RAD21	chr5:75370242-75370758	HCT-116	colon:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
20	ZNF143	chr5:75370354-75370684	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXM1	chr5:75370249-75370727	GM12878	blood:	n/a	n/a
22	CTCF	chr5:75370368-75370658	IMR90	lung:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
23	CTCF	chr5:75370437-75370607	SK-N-SH_RA	brain:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
24	CTCF	chr5:75370540-75370690	AG04450	lung:	n/a	n/a
25	RAD21	chr5:75370386-75370751	A549	lung:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
26	CTCF	chr5:75370500-75370650	AG04449	skin:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
27	CTCF	chr5:75370415-75370597	GM10266	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
28	CTCF	chr5:75370460-75370610	GM12865	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
29	CTCF	chr5:75370446-75370612	H1-hESC	embryonic stem cell:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
30	SMC3	chr5:75370380-75370696	K562	blood:	n/a	chr5:75370512-75370519
31	RAD21	chr5:75370415-75370654	K562	blood:	n/a	chr5:75370511-75370530
32	CTCF	chr5:75370340-75370614	K562	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
33	CTCF	chr5:75370330-75370681	K562	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
34	CTCF	chr5:75370394-75370634	K562	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
35	RAD21	chr5:75370270-75370755	MCF-7	breast:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
36	RAD21	chr5:75370280-75370721	GM12878	blood:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
37	CTCF	chr5:75370339-75370700	K562	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
38	CTCF	chr5:75370480-75370630	HepG2	liver:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
39	CTCF	chr5:75370460-75370610	HCPEpiC	choroid plexus:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
40	CTCF	chr5:75370460-75370610	HBMEC	blood vessel:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
41	CTCF	chr5:75370446-75370615	MCF-7	breast:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
42	CTCF	chr5:75370362-75370659	Medullo	brain:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
43	CTCF	chr5:75370460-75370610	A549	lung:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
44	CTCF	chr5:75370460-75370610	HUVEC	blood vessel:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
45	RAD21	chr5:75370330-75370723	H1-hESC	embryonic stem cell:	n/a	chr5:75370691-75370700 chr5:75370511-75370530
46	CTCF	chr5:75370445-75370619	GM12891	blood:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
47	SMC3	chr5:75370312-75370744	GM12878	blood:	n/a	chr5:75370512-75370519
48	RAD21	chr5:75370373-75370664	HepG2	liver:	n/a	chr5:75370511-75370530
49	CTCF	chr5:75370387-75370639	LNCaP	prostate:	n/a	chr5:75370513-75370522 chr5:75370512-75370533
50	RAD21	chr5:75370285-75370781	H1-hESC	embryonic stem cell:	n/a	chr5:75370691-75370700 chr5:75370511-75370530

No.	Distal block	Cell Line	Cell type
1	chr5:75370241..75371009-chr5:75551554..75552357,4	K562	blood:
2	chr5:75370056..75370744-chr5:75551849..75552754,4	MCF-7	breast:
3	chr5:75370258..75370917-chr5:75470691..75471438,2	MCF-7	breast:
4	chr5:75370186..75371274-chr5:75551816..75552790,4	MCF-7	breast:
5	chr5:75370002..75370997-chr5:75470399..75471572,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251342	TF binding region
ENSG00000249777	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13162056	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13174796	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1393205	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1423103	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423104	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1553310	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs183766	0.83[ASN][1000 genomes]
rs1910051	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254153	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2547455	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2547456	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258612	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258613	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258614	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731732	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2731733	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731735	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28621	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30191	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30196	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30197	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30198	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30199	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30202	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30204	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30205	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30206	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30249	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs39831	1.00[CHB][hapmap]
rs7378518	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7443455	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7443586	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs993914	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv4883	chr5:75360926-75373963	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv869885	chr5:75365786-75419656	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs30192	CTC-235G5.3	cis	Nerve Tibial	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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