Variant report

Variant	rs7720558
Chromosome Location	chr5:53560453-53560454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53559955..53564468-chr5:53605059..53610685,5	K562	blood:
2	chr5:53556262..53560678-chr5:53605289..53610112,7	K562	blood:
3	chr5:53560137..53562177-chr5:53606086..53608093,2	MCF-7	breast:
4	chr5:53560197..53562309-chr5:53565817..53568937,3	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10038691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043654	1.00[CEU][hapmap]
rs10056778	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10056892	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10062081	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10071081	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10072882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332105	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332445	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13354296	1.00[CEU][hapmap]
rs13360423	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16882537	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16882550	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28366402	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28553319	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28712367	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6889727	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72754233	1.00[EUR][1000 genomes]
rs72754234	1.00[EUR][1000 genomes]
rs72754235	1.00[EUR][1000 genomes]
rs72754240	1.00[EUR][1000 genomes]
rs72754242	1.00[EUR][1000 genomes]
rs72754250	1.00[EUR][1000 genomes]
rs72754252	1.00[EUR][1000 genomes]
rs72754254	1.00[EUR][1000 genomes]
rs72754268	1.00[EUR][1000 genomes]
rs72754270	1.00[EUR][1000 genomes]
rs72754271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72754272	1.00[EUR][1000 genomes]
rs72754274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72754275	1.00[EUR][1000 genomes]
rs72754280	1.00[EUR][1000 genomes]
rs72756244	1.00[EUR][1000 genomes]
rs72756250	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72756257	1.00[EUR][1000 genomes]
rs72756268	1.00[EUR][1000 genomes]
rs72756270	1.00[EUR][1000 genomes]
rs72756274	1.00[EUR][1000 genomes]
rs72756281	1.00[EUR][1000 genomes]
rs72756283	0.85[EUR][1000 genomes]
rs72756286	0.85[EUR][1000 genomes]
rs72756289	0.85[EUR][1000 genomes]
rs7715184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885300	1.00[EUR][1000 genomes]
rs9885301	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9885454	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
7	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
13	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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 lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
18	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv1031072	chr5:53490130-53698866	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv880304	chr5:53524508-53727092	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53537400-53575200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:53549400-53569800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:53553600-53568600	Weak transcription	Primary T cells from cord blood	blood
4	chr5:53555000-53572400	Weak transcription	Right Ventricle	heart
5	chr5:53555400-53566200	Weak transcription	HMEC	breast
6	chr5:53555600-53575800	Weak transcription	Primary B cells from cord blood	blood
7	chr5:53556000-53567400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:53556200-53562000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:53558000-53562400	Enhancers	K562	blood
10	chr5:53558800-53575600	Weak transcription	Aorta	Aorta
11	chr5:53559000-53562000	Weak transcription	Ovary	ovary
12	chr5:53559200-53560800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:53559400-53562800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr5:53559800-53572200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:53560000-53561000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:53560400-53560600	Enhancers	Left Ventricle	heart
17	chr5:53560400-53560600	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links