Variant report

Variant	rs16942787
Chromosome Location	chr16:65026260-65026261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10500505	0.81[ASN][1000 genomes]
rs11075558	0.81[ASN][1000 genomes]
rs11075559	0.81[ASN][1000 genomes]
rs1124695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1130821	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596107	0.80[ASN][1000 genomes]
rs12597175	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12598268	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[MEX][hapmap]
rs12599626	0.80[ASN][1000 genomes]
rs13334375	0.80[ASN][1000 genomes]
rs1390641	0.81[ASN][1000 genomes]
rs1402020	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs1496397	0.85[ASN][1000 genomes]
rs1520238	0.87[ASN][1000 genomes]
rs1554401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16956488	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs16968172	0.86[ASN][1000 genomes]
rs16968237	0.90[AMR][1000 genomes]
rs1896754	0.81[ASN][1000 genomes]
rs2195431	1.00[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3785315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57879848	0.81[ASN][1000 genomes]
rs58004552	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58245127	0.81[ASN][1000 genomes]
rs59208924	0.92[EUR][1000 genomes]
rs59407170	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59614634	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60424410	0.90[AMR][1000 genomes]
rs7190608	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73575990	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73579797	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8050545	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16942787	CCDC79	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:64991400-65032600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:65000800-65051000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:65003400-65034000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr16:65004800-65027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:65014200-65040200	Weak transcription	Fetal Intestine Small	intestine
6	chr16:65015000-65035000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:65016200-65032400	Weak transcription	Lung	lung
8	chr16:65016200-65040200	Weak transcription	Left Ventricle	heart
9	chr16:65017200-65041800	Weak transcription	Colon Smooth Muscle	Colon
10	chr16:65018000-65035600	Strong transcription	HSMM	muscle
11	chr16:65018400-65028400	Strong transcription	NH-A	brain
12	chr16:65018400-65028600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:65018800-65035600	Strong transcription	Osteobl	bone
14	chr16:65019000-65028000	Strong transcription	NHDF-Ad	bronchial
15	chr16:65019400-65026800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr16:65019600-65027800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:65020200-65028800	Strong transcription	NHLF	lung
18	chr16:65020400-65026800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr16:65020400-65027000	Strong transcription	Fetal Brain Female	brain
20	chr16:65021000-65034200	Weak transcription	Adipose Nuclei	Adipose
21	chr16:65021200-65038200	Weak transcription	Brain Germinal Matrix	brain
22	chr16:65021800-65027000	Strong transcription	Fetal Brain Male	brain
23	chr16:65022000-65041200	Weak transcription	Fetal Heart	heart
24	chr16:65022200-65037200	Weak transcription	Fetal Intestine Large	intestine
25	chr16:65022400-65027800	Strong transcription	Fetal Muscle Leg	muscle
26	chr16:65023400-65043200	Strong transcription	Fetal Lung	lung
27	chr16:65023600-65030000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:65023600-65039600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr16:65024200-65026800	Strong transcription	Fetal Kidney	kidney
30	chr16:65024400-65035000	Weak transcription	Brain Substantia Nigra	brain
31	chr16:65024600-65026800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:65024600-65031800	Weak transcription	Brain Hippocampus Middle	brain
33	chr16:65024800-65028400	Strong transcription	HMEC	breast
34	chr16:65025000-65026600	Strong transcription	Brain Cingulate Gyrus	brain
35	chr16:65025000-65026800	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr16:65025000-65026800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:65025000-65027000	Strong transcription	Brain Anterior Caudate	brain
38	chr16:65025200-65026600	Weak transcription	Right Ventricle	heart
39	chr16:65025200-65030800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:65025200-65037200	Weak transcription	Spleen	Spleen
41	chr16:65025400-65026600	Strong transcription	Brain Angular Gyrus	brain
42	chr16:65025400-65028400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr16:65025600-65027000	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr16:65025600-65027600	Strong transcription	HSMMtube	muscle
45	chr16:65025600-65028200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:65025600-65029600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr16:65025800-65027400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr16:65025800-65027800	Strong transcription	Ovary	ovary
49	chr16:65025800-65033000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr16:65025800-65051400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links