Variant report

Variant	rs1554401
Chromosome Location	chr16:65031338-65031339
allele	C/T
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];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1130821	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596107	0.81[ASN][1000 genomes]
rs12597175	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12598268	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap]
rs12599626	0.81[ASN][1000 genomes]
rs13334375	0.81[ASN][1000 genomes]
rs1390641	0.81[ASN][1000 genomes]
rs1402020	1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs1496397	0.86[ASN][1000 genomes]
rs1520238	0.88[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];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];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16968172	0.87[ASN][1000 genomes]
rs16968237	0.91[AMR][1000 genomes]
rs1896754	0.81[ASN][1000 genomes]
rs2195431	1.00[CEU][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3785315	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]
rs57879848	0.81[ASN][1000 genomes]
rs58004552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58245127	0.81[ASN][1000 genomes]
rs59208924	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59407170	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59614634	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60424410	0.91[AMR][1000 genomes]
rs7190608	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575990	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73579797	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8050545	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs1554401	CCDC79	cis	cerebellum	SCAN

Chromatin state (count:58 , 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	chr16:65014200-65040200	Weak transcription	Fetal Intestine Small	intestine
5	chr16:65015000-65035000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:65016200-65032400	Weak transcription	Lung	lung
7	chr16:65016200-65040200	Weak transcription	Left Ventricle	heart
8	chr16:65017200-65041800	Weak transcription	Colon Smooth Muscle	Colon
9	chr16:65018000-65035600	Strong transcription	HSMM	muscle
10	chr16:65018800-65035600	Strong transcription	Osteobl	bone
11	chr16:65021000-65034200	Weak transcription	Adipose Nuclei	Adipose
12	chr16:65021200-65038200	Weak transcription	Brain Germinal Matrix	brain
13	chr16:65022000-65041200	Weak transcription	Fetal Heart	heart
14	chr16:65022200-65037200	Weak transcription	Fetal Intestine Large	intestine
15	chr16:65023400-65043200	Strong transcription	Fetal Lung	lung
16	chr16:65023600-65039600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr16:65024400-65035000	Weak transcription	Brain Substantia Nigra	brain
18	chr16:65024600-65031800	Weak transcription	Brain Hippocampus Middle	brain
19	chr16:65025200-65037200	Weak transcription	Spleen	Spleen
20	chr16:65025800-65033000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:65025800-65051400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:65026000-65032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr16:65026000-65035800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr16:65026000-65037800	Weak transcription	Aorta	Aorta
25	chr16:65026000-65038600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr16:65026200-65033600	Weak transcription	Placenta	Placenta
27	chr16:65026200-65035200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr16:65026200-65035200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:65026600-65035200	Weak transcription	Brain Angular Gyrus	brain
30	chr16:65026800-65035000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:65027000-65031400	Weak transcription	Brain Anterior Caudate	brain
32	chr16:65027000-65036000	Weak transcription	Fetal Brain Female	brain
33	chr16:65027200-65035600	Weak transcription	HUVEC	blood vessel
34	chr16:65028400-65031600	Weak transcription	HMEC	breast
35	chr16:65029000-65037600	Weak transcription	Fetal Kidney	kidney
36	chr16:65029800-65035600	Strong transcription	NHDF-Ad	bronchial
37	chr16:65029800-65035800	Strong transcription	Fetal Muscle Leg	muscle
38	chr16:65030000-65032600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr16:65030000-65032600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:65030000-65032800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr16:65030000-65032800	Strong transcription	Ovary	ovary
42	chr16:65030000-65034600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr16:65030000-65034800	Strong transcription	Fetal Stomach	stomach
44	chr16:65030000-65035800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:65030200-65035200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr16:65030200-65035600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr16:65030400-65032800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:65030400-65034400	Strong transcription	NHLF	lung
49	chr16:65030400-65035400	Strong transcription	NH-A	brain
50	chr16:65030600-65031800	Strong transcription	Muscle Satellite Cultured Cells	--

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