Variant report

Variant	rs2171858
Chromosome Location	chr3:56798704-56798705
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10222681	0.93[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10428123	0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11130548	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2171855	0.82[EUR][1000 genomes]
rs2171857	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2276720	0.82[EUR][1000 genomes]
rs6794153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627647	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642971	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9812484	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs9825368	0.93[ASW][hapmap];0.82[AFR][1000 genomes]
rs9851853	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9871950	0.87[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9874011	0.85[EUR][1000 genomes]
rs9882898	1.00[CEU][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2171858	C3orf51	cis	cerebellum	SCAN
rs2171858	CCDC66	cis	parietal	SCAN

Chromatin state (count:89 , 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	chr3:56783400-56802800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:56783600-56802800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:56783800-56802800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:56789200-56805800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:56789400-56802800	Weak transcription	Ovary	ovary
7	chr3:56789400-56803200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:56789400-56803200	Weak transcription	Fetal Stomach	stomach
9	chr3:56789600-56801200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:56790200-56804600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:56790400-56803200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:56790400-56803200	Weak transcription	Spleen	Spleen
13	chr3:56792600-56809600	Weak transcription	Small Intestine	intestine
14	chr3:56792800-56801200	Strong transcription	Dnd41	blood
15	chr3:56792800-56803400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:56793000-56801000	Weak transcription	NH-A	brain
17	chr3:56793000-56802600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:56793000-56802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:56793000-56802800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:56793000-56803600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:56793000-56804600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:56793200-56799400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:56793200-56802800	Weak transcription	Fetal Kidney	kidney
24	chr3:56793200-56802800	Weak transcription	HMEC	breast
25	chr3:56793200-56803400	Weak transcription	NHEK	skin
26	chr3:56793200-56806000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:56793200-56807200	Weak transcription	HUVEC	blood vessel
28	chr3:56793200-56817400	Weak transcription	Hela-S3	cervix
29	chr3:56793400-56801200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:56793600-56805400	Weak transcription	Esophagus	oesophagus
31	chr3:56793600-56809600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:56793800-56803000	Weak transcription	HepG2	liver
33	chr3:56793800-56803600	Strong transcription	Fetal Thymus	thymus
34	chr3:56793800-56805600	Weak transcription	Primary B cells from cord blood	blood
35	chr3:56794000-56800200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:56794800-56802000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:56795400-56800600	Strong transcription	Primary T cells from cord blood	blood
38	chr3:56796000-56800000	Strong transcription	Thymus	Thymus
39	chr3:56796200-56801400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:56796400-56801200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:56796400-56803600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:56796400-56805400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:56796400-56807600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:56796600-56799200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:56796600-56800200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:56796600-56803200	Weak transcription	Lung	lung
47	chr3:56796600-56809800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:56796800-56799400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:56796800-56809600	Weak transcription	NHLF	lung
50	chr3:56796800-56816400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links