Variant report

Variant	rs62357525
Chromosome Location	chr5:58853698-58853699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58847787..58849644-chr5:58852199..58853846,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1035321	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10491440	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491441	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10491442	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514859	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950308	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11951110	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956402	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514190	1.00[ASN][1000 genomes]
rs12520633	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521279	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439074	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797996	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17798319	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081664	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56007967	1.00[ASN][1000 genomes]
rs62355561	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355562	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355581	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355582	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355584	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357524	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357530	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372240	1.00[ASN][1000 genomes]
rs72751212	1.00[ASN][1000 genomes]
rs72769726	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72769729	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs893190	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953302	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58836600-58854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58836800-58857400	Weak transcription	Primary B cells from cord blood	blood
3	chr5:58840200-58858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:58840400-58856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:58840800-58858600	Weak transcription	Fetal Kidney	kidney
6	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:58844400-58854600	Weak transcription	Fetal Lung	lung
8	chr5:58844800-58854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:58845200-58856200	Weak transcription	Hela-S3	cervix
10	chr5:58845600-58858200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:58850200-58858200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:58850400-58856400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:58850400-58860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:58850600-58856200	Weak transcription	Fetal Intestine Large	intestine
15	chr5:58850800-58853800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:58850800-58854800	Genic enhancers	A549	lung
17	chr5:58850800-58856200	Weak transcription	Fetal Intestine Small	intestine
18	chr5:58851600-58855600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:58851600-58858600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:58851800-58854400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:58851800-58854800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:58851800-58855200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:58851800-58855200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:58851800-58855400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:58851800-58856200	Weak transcription	Brain Angular Gyrus	brain
26	chr5:58851800-58856200	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:58851800-58857800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:58851800-58858600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:58851800-58859800	Weak transcription	Psoas Muscle	Psoas
30	chr5:58852000-58855600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:58852000-58855800	Weak transcription	Brain Substantia Nigra	brain
32	chr5:58853200-58853800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:58853200-58854600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:58853400-58854600	Weak transcription	Fetal Brain Male	brain
35	chr5:58853400-58858400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:58853400-58858400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:58853600-58853800	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links