Variant report

Variant	rs282526
Chromosome Location	chr3:56631273-56631274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10865997	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12486047	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496217	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12631156	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1388256	0.81[AMR][1000 genomes]
rs282524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282525	0.81[AMR][1000 genomes]
rs282532	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs282533	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282534	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs282537	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282538	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs282539	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282542	0.81[AMR][1000 genomes]
rs282543	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35349208	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3732513	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974218	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974222	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55810735	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66873962	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769055	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6799711	0.80[EUR][1000 genomes]
rs7639731	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7640995	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs955248	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9823685	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834064	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9873754	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9985317	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv2762329	chr3:56629678-56633892	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv2753446	chr3:56630460-56633660	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs282526	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
2	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
3	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
4	chr3:56600600-56640000	Weak transcription	NHLF	lung
5	chr3:56603000-56631600	Weak transcription	Fetal Brain Male	brain
6	chr3:56603200-56650400	Weak transcription	K562	blood
7	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
9	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
10	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
11	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
12	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
13	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
14	chr3:56609400-56638600	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:56616200-56633800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:56616400-56639400	Weak transcription	Lung	lung
17	chr3:56617200-56639200	Weak transcription	Thymus	Thymus
18	chr3:56617200-56639600	Weak transcription	Aorta	Aorta
19	chr3:56617400-56639800	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:56617400-56639800	Weak transcription	Dnd41	blood
21	chr3:56618800-56631800	Weak transcription	Fetal Intestine Small	intestine
22	chr3:56619200-56639600	Weak transcription	Gastric	stomach
23	chr3:56619200-56639800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:56623000-56639600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:56624800-56639600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:56624800-56639800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:56625200-56633200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:56625200-56639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:56625200-56639600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:56625200-56639600	Weak transcription	HMEC	breast
31	chr3:56625200-56640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:56625200-56640000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:56625200-56650400	Weak transcription	NHEK	skin
34	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:56625600-56639600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:56626200-56633000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
38	chr3:56626800-56631600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:56626800-56633400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:56627000-56631400	Strong transcription	Placenta	Placenta
41	chr3:56627000-56632600	Strong transcription	Liver	Liver
42	chr3:56627000-56632800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:56627000-56633000	Strong transcription	Fetal Intestine Large	intestine
44	chr3:56627200-56631600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:56627200-56633800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:56627400-56634000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr3:56627600-56631400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:56627600-56631400	Strong transcription	Adipose Nuclei	Adipose
49	chr3:56627600-56631600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:56627600-56639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links