Variant report

Variant	rs697076
Chromosome Location	chr5:58851811-58851812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10059809	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10065078	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1395335	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs1395336	0.88[CHB][hapmap]
rs1395337	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs296406	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs37579	0.94[ASW][hapmap];0.88[CHB][hapmap]
rs40215	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6858964	0.94[ASW][hapmap];0.88[CHB][hapmap]
rs702544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826435	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs697076	PDE4D	cis	cerebellum	SCAN

Chromatin state (count:35 , 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	chr5:58840400-58853200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:58840400-58856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:58840800-58858600	Weak transcription	Fetal Kidney	kidney
7	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:58844400-58854600	Weak transcription	Fetal Lung	lung
9	chr5:58844800-58854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58845200-58856200	Weak transcription	Hela-S3	cervix
11	chr5:58845600-58858200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:58850200-58858200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:58850400-58856400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:58850400-58860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:58850600-58856200	Weak transcription	Fetal Intestine Large	intestine
16	chr5:58850800-58853800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:58850800-58854800	Genic enhancers	A549	lung
18	chr5:58850800-58856200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:58851400-58852000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:58851400-58852000	Enhancers	Brain Substantia Nigra	brain
21	chr5:58851600-58852000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr5:58851600-58852000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr5:58851600-58853400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr5:58851600-58855600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:58851600-58858600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:58851800-58854400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:58851800-58854800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:58851800-58855200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:58851800-58855200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:58851800-58855400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:58851800-58856200	Weak transcription	Brain Angular Gyrus	brain
32	chr5:58851800-58856200	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:58851800-58857800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:58851800-58858600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:58851800-58859800	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links