Variant report

Variant	rs66741919
Chromosome Location	chr5:58822576-58822577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10514861	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10514862	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11746896	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16889907	0.80[AFR][1000 genomes]
rs16889920	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16889921	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6450520	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66605058	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67306207	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6885378	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7700365	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7706227	0.91[EUR][1000 genomes]
rs7707043	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7717819	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58810000-58823600	Weak transcription	Colon Smooth Muscle	Colon
2	chr5:58814600-58823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58815400-58830400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58815800-58823600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:58818800-58823800	Weak transcription	Stomach Mucosa	stomach
6	chr5:58819000-58832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:58820000-58831400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:58820200-58822800	Enhancers	Fetal Intestine Large	intestine
9	chr5:58820800-58823000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:58820800-58824600	Weak transcription	Psoas Muscle	Psoas
11	chr5:58821000-58822600	Enhancers	Fetal Intestine Small	intestine
12	chr5:58821000-58828600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:58821200-58823000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:58821400-58822600	Enhancers	HSMM	muscle
15	chr5:58821400-58822600	Enhancers	HSMMtube	muscle
16	chr5:58821400-58822600	Enhancers	NH-A	brain
17	chr5:58821400-58822800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:58821400-58823200	Enhancers	HUVEC	blood vessel
19	chr5:58821600-58823800	Weak transcription	Brain Substantia Nigra	brain
20	chr5:58821800-58823000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:58822200-58822600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:58822200-58823000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:58822200-58824000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr5:58822200-58838800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:58822400-58822800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:58822400-58823000	Enhancers	Fetal Brain Male	brain
27	chr5:58822400-58823800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:58822400-58823800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links