Variant report

Variant	rs188793
Chromosome Location	chr5:42889290-42889291
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	CTCF	chr5:42889241-42890020	SK-N-SH	brain:	n/a	chr5:42889616-42889623 chr5:42889610-42889626 chr5:42889609-42889627 chr5:42889604-42889625
2	GATA1	chr5:42889227-42889938	PBDE	blood:	n/a	chr5:42889582-42889592 chr5:42889584-42889594 chr5:42889584-42889591
3	SMC3	chr5:42889221-42890029	SK-N-SH	brain:	n/a	chr5:42889611-42889625
4	CTCF	chr5:42889275-42889892	HCT-116	colon:	n/a	chr5:42889616-42889623 chr5:42889610-42889626 chr5:42889609-42889627 chr5:42889604-42889625
5	CTCF	chr5:42889160-42889310	HRPEpiC	eye:	n/a	n/a
6	RAD21	chr5:42889273-42889949	HCT-116	colon:	n/a	chr5:42889607-42889626 chr5:42889616-42889625
7	CTCF	chr5:42889189-42890021	A549	lung:	n/a	chr5:42889616-42889623 chr5:42889610-42889626 chr5:42889609-42889627 chr5:42889604-42889625

No.	Distal block	Cell Line	Cell type
1	chr5:42881977..42885731-chr5:42887904..42891094,4	K562	blood:
2	chr5:42774206..42775075-chr5:42889129..42889866,2	K562	blood:
3	chr5:42767269..42768214-chr5:42889107..42889727,3	MCF-7	breast:
4	chr5:42745610..42746111-chr5:42889125..42890106,2	K562	blood:
5	chr5:42889184..42890160-chr5:42904939..42905716,2	K562	blood:
6	chr5:42057339..42057915-chr5:42889168..42890099,2	K562	blood:

Variant related genes	Relation type
SEPP1	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10036147	0.91[ASN][1000 genomes]
rs10036468	0.91[ASN][1000 genomes]
rs10044301	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10053947	0.92[ASN][1000 genomes]
rs10061198	0.91[ASN][1000 genomes]
rs10068961	0.92[ASN][1000 genomes]
rs10072017	0.97[ASN][1000 genomes]
rs12655096	0.92[ASN][1000 genomes]
rs12658770	0.87[ASN][1000 genomes]
rs12659760	0.93[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13156119	0.93[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13354920	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs160330	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1902100	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2098715	0.95[ASN][1000 genomes]
rs2548362	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2548364	0.85[EUR][1000 genomes]
rs2548365	0.86[EUR][1000 genomes]
rs2548366	0.86[EUR][1000 genomes]
rs2603622	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2603624	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28415991	0.92[ASN][1000 genomes]
rs309932	0.94[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309934	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309935	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309942	0.83[EUR][1000 genomes]
rs315246	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs315253	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs315262	0.88[YRI][hapmap]
rs315263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34917335	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34981544	0.91[ASN][1000 genomes]
rs371261	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs378235	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs378344	0.94[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs388214	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs420550	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs435312	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs446294	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4482913	0.91[ASN][1000 genomes]
rs4513706	0.93[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs453436	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451649	0.91[ASN][1000 genomes]
rs6451650	0.91[ASN][1000 genomes]
rs6451651	0.91[ASN][1000 genomes]
rs6451652	0.91[ASN][1000 genomes]
rs6451653	0.89[ASN][1000 genomes]
rs6451654	0.89[ASN][1000 genomes]
rs6864892	0.98[ASN][1000 genomes]
rs6867854	0.89[ASN][1000 genomes]
rs6875237	0.91[ASN][1000 genomes]
rs6881608	0.91[ASN][1000 genomes]
rs6885355	0.91[ASN][1000 genomes]
rs6886626	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895458	0.91[ASN][1000 genomes]
rs6895751	0.91[ASN][1000 genomes]
rs71627562	0.97[ASN][1000 genomes]
rs71627563	0.97[ASN][1000 genomes]
rs7701142	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7721545	0.94[ASN][1000 genomes]
rs9885101	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
2	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
3	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
4	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
5	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
8	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
9	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
10	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42878800-42890000	Enhancers	HepG2	liver
2	chr5:42885800-42889600	Enhancers	Fetal Intestine Large	intestine
3	chr5:42886000-42890000	Enhancers	Fetal Intestine Small	intestine
4	chr5:42887400-42890000	Enhancers	Liver	Liver
5	chr5:42887600-42894400	Weak transcription	K562	blood
6	chr5:42888000-42889600	Enhancers	Adipose Nuclei	Adipose
7	chr5:42888200-42889600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:42889200-42889600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links