Variant report

Variant	rs13190010
Chromosome Location	chr5:53547784-53547785
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53544706..53547998-chr5:53684004..53686968,3	K562	blood:
2	chr5:53534084..53536973-chr5:53546883..53548612,2	K562	blood:
3	chr5:53546187..53547942-chr5:53555155..53557445,2	K562	blood:
4	chr5:53543864..53552129-chr5:53602110..53608167,13	MCF-7	breast:
5	chr5:53536985..53551112-chr5:53602807..53614557,36	K562	blood:
6	chr5:53546187..53549034-chr5:53553826..53556655,3	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction
ENSG00000249069	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10041550	1.00[ASN][1000 genomes]
rs10041555	1.00[ASN][1000 genomes]
rs10043654	1.00[ASN][1000 genomes]
rs10074776	0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs11739911	1.00[ASN][1000 genomes]
rs11740324	1.00[ASN][1000 genomes]
rs11743996	1.00[ASN][1000 genomes]
rs11957249	1.00[ASN][1000 genomes]
rs13155990	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156373	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157497	1.00[ASN][1000 genomes]
rs13159846	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162552	1.00[ASN][1000 genomes]
rs13171042	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172689	1.00[ASN][1000 genomes]
rs13182438	1.00[ASN][1000 genomes]
rs13183386	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354296	1.00[ASN][1000 genomes]
rs13354604	1.00[ASN][1000 genomes]
rs13356576	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882546	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882575	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882580	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882609	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17321792	1.00[ASN][1000 genomes]
rs17413044	1.00[ASN][1000 genomes]
rs2897654	0.92[EUR][1000 genomes]
rs34171374	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34430216	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34623175	0.90[EUR][1000 genomes]
rs34883270	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889997	1.00[ASN][1000 genomes]
rs35105742	1.00[ASN][1000 genomes]
rs35486183	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35503723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646158	1.00[ASN][1000 genomes]
rs35702491	1.00[ASN][1000 genomes]
rs35765393	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36104210	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846492	1.00[ASN][1000 genomes]
rs62355131	1.00[ASN][1000 genomes]
rs6450182	0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs66541213	1.00[ASN][1000 genomes]
rs67009061	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67012013	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67089826	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67894567	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859542	1.00[ASN][1000 genomes]
rs6879661	1.00[MEX][hapmap]
rs6891928	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892938	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71622108	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71622110	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752163	1.00[ASN][1000 genomes]
rs72757857	1.00[ASN][1000 genomes]
rs73120767	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704922	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733332	0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs9292043	1.00[ASN][1000 genomes]
rs9292044	1.00[ASN][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53523400-53547800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:53537400-53575200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:53538000-53550800	Weak transcription	Gastric	stomach
4	chr5:53542600-53550400	Weak transcription	Right Ventricle	heart
5	chr5:53543200-53556600	Weak transcription	Fetal Lung	lung
6	chr5:53543600-53553800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:53544200-53548000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:53545000-53549000	Enhancers	Fetal Heart	heart
9	chr5:53545600-53551600	Enhancers	K562	blood
10	chr5:53545600-53553000	Weak transcription	HMEC	breast
11	chr5:53545800-53547800	Weak transcription	Stomach Mucosa	stomach
12	chr5:53545800-53550600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:53545800-53553200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:53545800-53553800	Weak transcription	Lung	lung
15	chr5:53546000-53553800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:53546200-53553600	Weak transcription	GM12878-XiMat	blood
17	chr5:53546400-53549000	Enhancers	Fetal Intestine Large	intestine
18	chr5:53546600-53550400	Weak transcription	Right Atrium	heart
19	chr5:53546600-53550400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:53546800-53548200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:53546800-53548400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:53546800-53549400	Enhancers	Fetal Intestine Small	intestine
23	chr5:53546800-53550400	Weak transcription	Left Ventricle	heart
24	chr5:53546800-53550400	Weak transcription	Psoas Muscle	Psoas
25	chr5:53546800-53553200	Weak transcription	Small Intestine	intestine
26	chr5:53547200-53547800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr5:53547400-53547800	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr5:53547400-53550600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:53547600-53548000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:53547600-53548000	Enhancers	Duodenum Mucosa	Duodenum
31	chr5:53547600-53548200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr5:53547600-53548200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr5:53547600-53548400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr5:53547600-53549200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links