Variant report

Variant	rs58258059
Chromosome Location	chr13:50161281-50161282
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	NFIC	chr13:50161202-50162028	HepG2	liver:	n/a	n/a
2	FOXA1	chr13:50161188-50162020	HepG2	liver:	n/a	chr13:50161818-50161830
3	FOS	chr13:50161056-50161771	MCF10A-Er-Src	breast:	n/a	n/a
4	RCOR1	chr13:50160917-50161956	IMR90	lung:	n/a	n/a
5	STAT3	chr13:50160886-50161761	MCF10A-Er-Src	breast:	n/a	n/a
6	HDAC2	chr13:50161274-50161975	HepG2	liver:	n/a	chr13:50161751-50161765 chr13:50161830-50161844 chr13:50161752-50161766
7	TEAD4	chr13:50161261-50162113	HepG2	liver:	n/a	chr13:50161609-50161618
8	FOXA1	chr13:50160755-50162015	HepG2	liver:	n/a	chr13:50160757-50160769 chr13:50161818-50161830
9	STAT3	chr13:50160985-50161761	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr13:50161088-50161742	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXA2	chr13:50161280-50162009	HepG2	liver:	n/a	chr13:50161818-50161830
12	STAT3	chr13:50160738-50161761	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr13:50161240-50162039	HepG2	liver:	n/a	n/a
14	FOXA2	chr13:50161059-50162129	HepG2	liver:	n/a	chr13:50161818-50161830
15	TCF7L2	chr13:50161253-50161957	HepG2	liver:	n/a	n/a
16	MBD4	chr13:50161274-50162048	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:50087217..50089138-chr13:50160277..50162233,2	MCF-7	breast:
2	chr13:50016992..50019784-chr13:50159235..50161344,2	K562	blood:
3	chr13:50158705..50160311-chr13:50160787..50163577,2	K562	blood:
4	chr13:50016508..50019619-chr13:50158297..50162493,5	MCF-7	breast:
5	chr13:50018091..50020783-chr13:50160403..50162609,2	MCF-7	breast:
6	chr13:50091935..50095583-chr13:50159811..50161648,3	MCF-7	breast:

Variant related genes	Relation type
RCBTB1	TF binding region
ENSG00000215462	Chromatin interaction
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136144	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs57884356	1.00[AMR][1000 genomes]
rs58284306	1.00[AMR][1000 genomes]
rs61061574	1.00[AMR][1000 genomes]
rs7317736	1.00[AMR][1000 genomes]
rs7323574	1.00[AMR][1000 genomes]
rs73491209	1.00[AMR][1000 genomes]
rs73491212	1.00[AMR][1000 genomes]
rs73491222	1.00[AMR][1000 genomes]
rs73491238	1.00[AMR][1000 genomes]
rs73491240	1.00[AMR][1000 genomes]
rs73491263	1.00[AMR][1000 genomes]
rs73491278	1.00[AMR][1000 genomes]
rs73491283	1.00[AMR][1000 genomes]
rs73491286	1.00[AMR][1000 genomes]
rs73493208	1.00[AMR][1000 genomes]
rs73493213	1.00[AMR][1000 genomes]
rs73493222	1.00[AMR][1000 genomes]
rs73493244	1.00[AMR][1000 genomes]
rs73493248	1.00[AMR][1000 genomes]
rs73493257	1.00[AMR][1000 genomes]
rs73493259	1.00[AMR][1000 genomes]
rs73493264	1.00[AMR][1000 genomes]
rs73493297	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73495301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
15	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50160400-50161400	Weak transcription	HSMM	muscle
2	chr13:50160400-50161800	Enhancers	Muscle Satellite Cultured Cells	--
3	chr13:50160400-50161800	Flanking Active TSS	HepG2	liver
4	chr13:50160400-50161800	Enhancers	HSMMtube	muscle
5	chr13:50160400-50161800	Enhancers	NHLF	lung
6	chr13:50160400-50161800	Enhancers	Osteobl	bone
7	chr13:50160400-50162000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:50160400-50162200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr13:50160600-50161400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:50160600-50161400	Enhancers	Brain Anterior Caudate	brain
11	chr13:50160600-50161600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:50160600-50161600	Enhancers	Liver	Liver
13	chr13:50160600-50161600	Enhancers	A549	lung
14	chr13:50160600-50161600	Weak transcription	K562	blood
15	chr13:50160600-50161800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:50160600-50161800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:50160600-50161800	Enhancers	HUVEC	blood vessel
18	chr13:50160600-50162000	Enhancers	Hela-S3	cervix
19	chr13:50160600-50162400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:50160600-50162400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr13:50160600-50162400	Enhancers	HMEC	breast
22	chr13:50160600-50162600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:50160600-50169200	Weak transcription	Esophagus	oesophagus
24	chr13:50160800-50161400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr13:50160800-50161400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:50160800-50161400	Weak transcription	Psoas Muscle	Psoas
27	chr13:50161000-50161600	Weak transcription	Fetal Heart	heart
28	chr13:50161000-50161800	Enhancers	NH-A	brain
29	chr13:50161000-50161800	Flanking Active TSS	NHEK	skin
30	chr13:50161200-50161600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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