Variant report

Variant	rs9882898
Chromosome Location	chr3:56805376-56805377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10222681	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10428123	0.88[MEX][hapmap]
rs11130548	0.87[EUR][1000 genomes]
rs2171857	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2171858	1.00[CEU][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6794153	1.00[CEU][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7627647	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9812484	0.93[CEU][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9851853	0.92[CEU][hapmap]
rs9871950	0.87[MEX][hapmap];0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876818	chr3:56805376-56924711	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9882898	CCDC66	cis	parietal	SCAN
rs9882898	CCDC66	cis	cerebellum	SCAN
rs9882898	C3orf51	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:56789200-56805800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:56792600-56809600	Weak transcription	Small Intestine	intestine
4	chr3:56793200-56806000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:56793200-56807200	Weak transcription	HUVEC	blood vessel
6	chr3:56793200-56817400	Weak transcription	Hela-S3	cervix
7	chr3:56793600-56805400	Weak transcription	Esophagus	oesophagus
8	chr3:56793600-56809600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:56793800-56805600	Weak transcription	Primary B cells from cord blood	blood
10	chr3:56796400-56805400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:56796400-56807600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:56796600-56809800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:56796800-56809600	Weak transcription	NHLF	lung
14	chr3:56796800-56816400	Weak transcription	Colonic Mucosa	Colon
15	chr3:56797200-56809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:56797400-56805400	Weak transcription	Gastric	stomach
17	chr3:56797600-56811400	Weak transcription	Stomach Mucosa	stomach
18	chr3:56799000-56815800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:56800400-56807000	Weak transcription	Fetal Intestine Large	intestine
20	chr3:56800600-56805600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:56800800-56808200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:56800800-56809000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:56801000-56805400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:56801600-56808200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:56801800-56805800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:56802000-56806400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:56802000-56806600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:56802600-56805600	Strong transcription	Primary T cells from cord blood	blood
29	chr3:56802600-56811800	Strong transcription	Dnd41	blood
30	chr3:56802800-56807400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:56802800-56807600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:56802800-56808000	Strong transcription	HMEC	breast
33	chr3:56803200-56807400	Strong transcription	Lung	lung
34	chr3:56803200-56808600	Strong transcription	Fetal Stomach	stomach
35	chr3:56803200-56809200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:56803200-56809600	Strong transcription	Thymus	Thymus
37	chr3:56803400-56806400	Strong transcription	NHEK	skin
38	chr3:56803400-56810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:56803600-56805400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:56803600-56805400	Weak transcription	Spleen	Spleen
41	chr3:56803600-56807000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr3:56803600-56807400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:56803600-56807600	Weak transcription	Ovary	ovary
44	chr3:56803600-56809600	Weak transcription	Fetal Kidney	kidney
45	chr3:56803800-56805400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:56803800-56805400	Weak transcription	Pancreas	Pancrea
47	chr3:56803800-56807400	Weak transcription	Fetal Brain Male	brain
48	chr3:56804000-56805400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:56804000-56805400	Weak transcription	Brain Anterior Caudate	brain
50	chr3:56804000-56805400	Weak transcription	Colon Smooth Muscle	Colon

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