Variant report

Variant	rs291117
Chromosome Location	chr5:58859925-58859926
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:58853948..58856765-chr5:58857609..58860199,2	MCF-7	breast:
2	chr5:58858064..58860308-chr5:58864549..58867326,2	K562	blood:
3	chr5:58843792..58846510-chr5:58858792..58861752,2	MCF-7	breast:
4	chr5:58853827..58855352-chr5:58858550..58860453,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs159393	1.00[ASN][1000 genomes]
rs294476	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs294503	1.00[ASN][1000 genomes]
rs295977	0.82[ASN][1000 genomes]
rs41404047	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:58850400-58860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:58854600-58861600	Weak transcription	Fetal Brain Female	brain
4	chr5:58855600-58863000	Enhancers	Primary B cells from peripheral blood	blood
5	chr5:58856600-58864000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:58856600-58865400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:58857800-58860200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:58857800-58860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:58858200-58860000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:58858200-58860000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:58858200-58860200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr5:58858200-58860400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:58858400-58860000	Enhancers	HMEC	breast
14	chr5:58858600-58860000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr5:58858600-58860200	Enhancers	HUVEC	blood vessel
16	chr5:58858600-58861400	Enhancers	Stomach Mucosa	stomach
17	chr5:58858600-58862600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:58858800-58860200	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr5:58858800-58861600	Enhancers	Thymus	Thymus
20	chr5:58859000-58860200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:58859000-58860400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr5:58859000-58860600	Weak transcription	Gastric	stomach
23	chr5:58859200-58860200	Enhancers	GM12878-XiMat	blood
24	chr5:58859200-58860800	Weak transcription	Fetal Intestine Small	intestine
25	chr5:58859200-58861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:58859200-58883400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:58859400-58860600	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:58859400-58865200	Weak transcription	Brain Substantia Nigra	brain
29	chr5:58859400-58870400	Weak transcription	Fetal Intestine Large	intestine
30	chr5:58859400-58871600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:58859400-58884000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:58859600-58860600	Enhancers	Primary B cells from cord blood	blood
33	chr5:58859600-58860600	Genic enhancers	A549	lung
34	chr5:58859600-58862600	Enhancers	Hela-S3	cervix
35	chr5:58859600-58864800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:58859800-58860600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:58859800-58860600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:58859800-58860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:58859800-58860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:58859800-58861800	Enhancers	Psoas Muscle	Psoas
41	chr5:58859800-58863200	Weak transcription	Fetal Lung	lung
42	chr5:58859800-58864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:58859800-58865400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:58859800-58873800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links