Variant report

Variant	rs3785315
Chromosome Location	chr16:65005395-65005396
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:34)

rs_ID	r²[population]
rs10500505	0.86[ASN][1000 genomes]
rs11075558	0.86[ASN][1000 genomes]
rs11075559	0.86[ASN][1000 genomes]
rs1124695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1130821	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12596107	0.85[ASN][1000 genomes]
rs12597175	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12598268	0.84[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.91[YRI][hapmap]
rs12599626	0.85[ASN][1000 genomes]
rs13334375	0.85[ASN][1000 genomes]
rs1390641	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1402020	1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1496397	0.91[ASN][1000 genomes]
rs1520238	0.93[ASN][1000 genomes]
rs1554401	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16942787	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]
rs16956488	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16968172	0.91[ASN][1000 genomes]
rs16968237	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1896754	0.86[ASN][1000 genomes]
rs2195431	1.00[CEU][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs57879848	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs58004552	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58245127	0.86[ASN][1000 genomes]
rs59208924	0.93[EUR][1000 genomes]
rs59407170	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59614634	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60424410	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62042187	0.83[AFR][1000 genomes]
rs7184863	0.80[ASN][1000 genomes]
rs7190608	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73575990	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73579797	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8050545	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs3785315	CCDC79	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:64984800-65005400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr16:64985000-65005800	Weak transcription	Aorta	Aorta
3	chr16:64985000-65011000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:64985400-65005800	Weak transcription	Spleen	Spleen
5	chr16:64985400-65015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr16:64991400-65032600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr16:64998000-65024800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:64998400-65014800	Weak transcription	HUVEC	blood vessel
9	chr16:64999200-65010200	Strong transcription	HSMM	muscle
10	chr16:64999200-65017800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr16:64999200-65017800	Strong transcription	NH-A	brain
12	chr16:65000800-65051000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:65001200-65006800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr16:65001200-65007000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr16:65001200-65012600	Strong transcription	Fetal Lung	lung
16	chr16:65002200-65005400	Enhancers	Fetal Heart	heart
17	chr16:65002400-65015200	Weak transcription	Left Ventricle	heart
18	chr16:65002600-65005800	Weak transcription	Fetal Stomach	stomach
19	chr16:65002600-65016000	Weak transcription	Brain Angular Gyrus	brain
20	chr16:65003000-65005400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr16:65003000-65006200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr16:65003000-65007400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr16:65003000-65008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr16:65003200-65008400	Strong transcription	NHLF	lung
25	chr16:65003400-65006800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr16:65003400-65034000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr16:65003600-65005800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr16:65003600-65006800	Strong transcription	NHDF-Ad	bronchial
29	chr16:65003800-65006600	Strong transcription	Ovary	ovary
30	chr16:65003800-65016000	Weak transcription	Brain Hippocampus Middle	brain
31	chr16:65004000-65006400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:65004000-65006600	Weak transcription	Esophagus	oesophagus
33	chr16:65004000-65006800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr16:65004000-65007000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr16:65004200-65005800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr16:65004200-65006600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:65004200-65006600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr16:65004200-65006600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr16:65004200-65006800	Strong transcription	Brain Anterior Caudate	brain
40	chr16:65004200-65006800	Strong transcription	HSMMtube	muscle
41	chr16:65004200-65007000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr16:65004200-65008800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr16:65004200-65009600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr16:65004200-65017400	Strong transcription	Osteobl	bone
45	chr16:65004400-65005800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr16:65004400-65006600	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr16:65004400-65006600	Strong transcription	HMEC	breast
48	chr16:65004400-65007000	Strong transcription	Fetal Intestine Large	intestine
49	chr16:65004400-65011800	Strong transcription	Fetal Muscle Leg	muscle
50	chr16:65004600-65006200	Strong transcription	Fetal Brain Female	brain

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