Variant report

Variant	rs17369487
Chromosome Location	chr5:112221005-112221006
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112196522..112198362-chr5:112219263..112221236,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZRSR1-3	chr5:112220791-112221442	NONHSAT103249

Variant related genes	Relation type
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12521395	0.89[AMR][1000 genomes]
rs13185006	1.00[AMR][1000 genomes]
rs17135067	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17135193	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17285666	1.00[CEU][hapmap]
rs17286230	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17290064	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17310536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17311019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17311096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17359859	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17360045	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17360289	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17369211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17370550	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17371015	0.93[EUR][1000 genomes]
rs1833560	0.86[EUR][1000 genomes]
rs4235776	1.00[AMR][1000 genomes]
rs4235780	1.00[AMR][1000 genomes]
rs4235781	1.00[AMR][1000 genomes]
rs4235782	1.00[AMR][1000 genomes]
rs4235783	1.00[AMR][1000 genomes]
rs4235784	1.00[AMR][1000 genomes]
rs4260661	1.00[AMR][1000 genomes]
rs4519915	1.00[AMR][1000 genomes]
rs4705534	1.00[AMR][1000 genomes]
rs4705535	0.89[AMR][1000 genomes]
rs4705757	1.00[AMR][1000 genomes]
rs55684649	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55771309	0.81[EUR][1000 genomes]
rs55771959	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55798475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55901036	1.00[AMR][1000 genomes]
rs55940904	1.00[AMR][1000 genomes]
rs56023848	1.00[AMR][1000 genomes]
rs56052440	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56155803	0.81[EUR][1000 genomes]
rs56194248	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56218335	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56235416	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56265422	1.00[AMR][1000 genomes]
rs56320268	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56321569	0.93[EUR][1000 genomes]
rs56328836	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56405915	0.81[EUR][1000 genomes]
rs57043077	0.93[EUR][1000 genomes]
rs60532731	0.81[EUR][1000 genomes]
rs6594657	1.00[AMR][1000 genomes]
rs6594658	1.00[AMR][1000 genomes]
rs6862944	1.00[AMR][1000 genomes]
rs6872473	1.00[AMR][1000 genomes]
rs6881198	0.89[AMR][1000 genomes]
rs6881233	1.00[AMR][1000 genomes]
rs6881426	0.89[AMR][1000 genomes]
rs6897972	1.00[AMR][1000 genomes]
rs73216225	0.93[EUR][1000 genomes]
rs73220038	0.93[EUR][1000 genomes]
rs73220063	0.86[EUR][1000 genomes]
rs7704566	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7706745	1.00[AMR][1000 genomes]
rs7728495	1.00[AMR][1000 genomes]
rs7728766	0.93[EUR][1000 genomes]
rs7730441	0.86[EUR][1000 genomes]
rs878074	1.00[AMR][1000 genomes]
rs878075	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
4	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:112210600-112225000	Strong transcription	Liver	Liver
11	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr5:112211200-112222600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:112211200-112240000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:112211800-112223400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr5:112211800-112239200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:112212400-112225200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:112212400-112225400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:112213000-112223000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:112213000-112223200	Strong transcription	Fetal Lung	lung
24	chr5:112213000-112223200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr5:112213000-112224600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:112213200-112222800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr5:112213200-112223200	Strong transcription	Brain Germinal Matrix	brain
28	chr5:112213200-112223400	Strong transcription	Adipose Nuclei	Adipose
29	chr5:112213200-112223400	Strong transcription	Fetal Brain Female	brain
30	chr5:112213200-112229400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:112213600-112223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:112213800-112225000	Strong transcription	Fetal Intestine Large	intestine
33	chr5:112214000-112223400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:112214000-112224400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:112214200-112232200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:112214800-112223400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:112214800-112223400	Strong transcription	Fetal Thymus	thymus
38	chr5:112214800-112226600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:112214800-112234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr5:112215000-112223000	Strong transcription	Fetal Stomach	stomach
41	chr5:112215200-112223000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:112215200-112224800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:112215400-112222600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr5:112215400-112223000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:112215400-112223200	Strong transcription	HMEC	breast
47	chr5:112215400-112223400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:112215400-112223400	Strong transcription	Placenta	Placenta
49	chr5:112215800-112222200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr5:112215800-112222800	Strong transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links