Variant report

Variant	rs16890078
Chromosome Location	chr5:58957322-58957323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:17875088..17875599-chr5:58957118..58957618,2	Hela-S3	cervix:
2	chr5:58803367..58805536-chr5:58956722..58959458,2	MCF-7	breast:
3	chr5:58956441..58957361-chr5:58968943..58969531,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10045168	0.83[ASN][1000 genomes]
rs10052367	0.83[ASN][1000 genomes]
rs10052716	0.83[ASN][1000 genomes]
rs10062267	0.83[ASN][1000 genomes]
rs10065233	0.83[ASN][1000 genomes]
rs10073739	0.83[ASN][1000 genomes]
rs10076914	0.83[ASN][1000 genomes]
rs10472114	0.83[ASN][1000 genomes]
rs11741470	0.83[ASN][1000 genomes]
rs13164391	0.83[ASN][1000 genomes]
rs13168643	0.83[ASN][1000 genomes]
rs13177163	0.83[ASN][1000 genomes]
rs13361053	0.83[ASN][1000 genomes]
rs159615	0.83[ASN][1000 genomes]
rs159618	0.83[ASN][1000 genomes]
rs159621	0.83[ASN][1000 genomes]
rs173944	0.83[ASN][1000 genomes]
rs194368	0.83[ASN][1000 genomes]
rs1960603	0.83[ASN][1000 genomes]
rs256349	0.83[ASN][1000 genomes]
rs256351	0.83[ASN][1000 genomes]
rs256354	0.83[ASN][1000 genomes]
rs35302677	0.83[ASN][1000 genomes]
rs56063442	0.83[ASN][1000 genomes]
rs58802762	0.83[ASN][1000 genomes]
rs61229155	0.83[ASN][1000 genomes]
rs62370463	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62370466	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62370490	0.83[ASN][1000 genomes]
rs62370491	0.83[ASN][1000 genomes]
rs62370494	0.83[ASN][1000 genomes]
rs62370495	0.83[ASN][1000 genomes]
rs62370496	0.83[ASN][1000 genomes]
rs62370498	0.83[ASN][1000 genomes]
rs62370501	0.83[ASN][1000 genomes]
rs62370505	0.83[ASN][1000 genomes]
rs62370506	0.83[ASN][1000 genomes]
rs62370529	0.83[ASN][1000 genomes]
rs6865975	0.83[ASN][1000 genomes]
rs72751228	0.83[ASN][1000 genomes]
rs7706277	0.83[ASN][1000 genomes]
rs7706573	0.83[ASN][1000 genomes]
rs7732908	0.83[ASN][1000 genomes]
rs9292212	0.83[ASN][1000 genomes]
rs9292213	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv462190	chr5:58936943-59023870	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv598258	chr5:58936943-59023870	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58948000-58961600	Weak transcription	Gastric	stomach
2	chr5:58952000-58957600	Weak transcription	Liver	Liver
3	chr5:58952400-58957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:58954400-58957800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:58954600-58957800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:58954600-58958600	Enhancers	Stomach Mucosa	stomach
7	chr5:58954800-58957800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:58954800-58958000	Enhancers	Primary hematopoietic stem cells	blood
9	chr5:58954800-58958400	Enhancers	Fetal Intestine Small	intestine
10	chr5:58955000-58957400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:58955000-58958000	Enhancers	Primary B cells from cord blood	blood
12	chr5:58955400-58957800	Enhancers	Colon Smooth Muscle	Colon
13	chr5:58955800-58957800	Enhancers	Rectal Smooth Muscle	rectum
14	chr5:58956000-58957600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:58956000-58957600	Weak transcription	Aorta	Aorta
16	chr5:58956000-58959000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:58956000-58959000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:58956200-58958400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:58956400-58957400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:58956400-58957800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr5:58956400-58957800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr5:58956400-58958000	Enhancers	HUVEC	blood vessel
23	chr5:58956400-58958400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:58956400-58958400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr5:58956400-58958600	Enhancers	Hela-S3	cervix
26	chr5:58956400-58958600	Enhancers	HSMMtube	muscle
27	chr5:58956600-58957600	Weak transcription	Fetal Intestine Large	intestine
28	chr5:58956600-58957600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:58956600-58957600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:58956600-58957800	Enhancers	Duodenum Mucosa	Duodenum
31	chr5:58956600-58957800	Weak transcription	HSMM	muscle
32	chr5:58956600-58958000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr5:58956600-58958200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr5:58956600-58958200	Enhancers	Brain Cingulate Gyrus	brain
35	chr5:58956600-58958400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr5:58956800-58957800	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:58957000-58957400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:58957000-58957400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:58957000-58958000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:58957000-58958200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:58957000-58958200	Enhancers	Small Intestine	intestine
42	chr5:58957200-58957400	Flanking Active TSS	A549	lung
43	chr5:58957200-58957800	Enhancers	Adipose Nuclei	Adipose
44	chr5:58957200-58958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr5:58957200-58958000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:58957200-58958000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:58957200-58958000	Enhancers	GM12878-XiMat	blood
48	chr5:58957200-58958200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:58957200-58958200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:58957200-58958200	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links