Variant report

Variant	rs4780419
Chromosome Location	chr16:12368668-12368669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11075057	0.84[EUR][1000 genomes]
rs11075058	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11075059	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11075062	0.82[GIH][hapmap]
rs11639640	0.88[EUR][1000 genomes]
rs11644788	0.89[EUR][1000 genomes]
rs11648926	0.80[EUR][1000 genomes]
rs11649626	0.88[EUR][1000 genomes]
rs11861914	0.91[EUR][1000 genomes]
rs12148953	0.83[EUR][1000 genomes]
rs12445263	0.85[EUR][1000 genomes]
rs12445569	0.86[EUR][1000 genomes]
rs12446650	0.85[EUR][1000 genomes]
rs12448443	0.87[EUR][1000 genomes]
rs13335852	0.89[EUR][1000 genomes]
rs16959318	0.81[EUR][1000 genomes]
rs176717	0.83[EUR][1000 genomes]
rs17697005	0.86[EUR][1000 genomes]
rs17764604	0.86[EUR][1000 genomes]
rs2089251	0.83[EUR][1000 genomes]
rs209849	0.86[EUR][1000 genomes]
rs209850	0.86[EUR][1000 genomes]
rs209853	0.85[EUR][1000 genomes]
rs209855	0.84[EUR][1000 genomes]
rs2856771	0.86[EUR][1000 genomes]
rs35818743	0.85[EUR][1000 genomes]
rs476267	0.82[EUR][1000 genomes]
rs4780417	0.88[EUR][1000 genomes]
rs4780418	0.85[EUR][1000 genomes]
rs4781200	0.86[EUR][1000 genomes]
rs4781201	0.86[EUR][1000 genomes]
rs4781202	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4781209	0.82[GIH][hapmap]
rs4781214	0.85[GIH][hapmap]
rs544598	0.83[EUR][1000 genomes]
rs6498274	0.89[EUR][1000 genomes]
rs7189386	0.85[EUR][1000 genomes]
rs7189945	0.85[EUR][1000 genomes]
rs7190509	0.82[GIH][hapmap]
rs7191442	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7192102	0.85[EUR][1000 genomes]
rs7194718	0.90[EUR][1000 genomes]
rs7194981	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7195058	0.83[EUR][1000 genomes]
rs7195520	0.82[EUR][1000 genomes]
rs7197417	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7199556	0.85[EUR][1000 genomes]
rs7200289	0.87[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7204209	0.86[EUR][1000 genomes]
rs7204333	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7500910	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8046012	0.87[EUR][1000 genomes]
rs8051758	0.81[EUR][1000 genomes]
rs8061549	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8063991	0.86[EUR][1000 genomes]
rs868773	0.88[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs869289	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs905950	0.89[EUR][1000 genomes]
rs9284322	0.85[GIH][hapmap]
rs9630612	0.89[EUR][1000 genomes]
rs9921551	0.94[ASN][1000 genomes]
rs9927705	0.84[EUR][1000 genomes]
rs9928214	0.80[EUR][1000 genomes]
rs9930625	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9937220	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4780419	C16orf63	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12308000-12371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr16:12309800-12371200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr16:12323400-12394200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr16:12323800-12373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:12330800-12373000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:12334600-12371800	Weak transcription	Adipose Nuclei	Adipose
7	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
8	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
9	chr16:12348200-12371400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:12350200-12371600	Weak transcription	GM12878-XiMat	blood
11	chr16:12351200-12373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:12351200-12382800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:12354800-12382800	Weak transcription	Gastric	stomach
14	chr16:12355200-12372000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr16:12356000-12390200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:12356400-12378000	Weak transcription	Spleen	Spleen
17	chr16:12356600-12371600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:12356600-12372800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:12356800-12371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:12356800-12373000	Weak transcription	Fetal Intestine Small	intestine
21	chr16:12356800-12373000	Weak transcription	Fetal Stomach	stomach
22	chr16:12357200-12383000	Weak transcription	Esophagus	oesophagus
23	chr16:12357400-12370400	Weak transcription	Aorta	Aorta
24	chr16:12357400-12373000	Weak transcription	Liver	Liver
25	chr16:12358600-12373200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr16:12359200-12377400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr16:12359400-12380800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:12359800-12418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr16:12361200-12372600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr16:12361800-12383000	Weak transcription	Fetal Muscle Leg	muscle
31	chr16:12362000-12374600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr16:12362000-12382600	Weak transcription	Placenta	Placenta
33	chr16:12362800-12370400	Weak transcription	Primary T cells from cord blood	blood
34	chr16:12365000-12371800	Weak transcription	Primary B cells from cord blood	blood
35	chr16:12365200-12374000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:12365200-12374200	Weak transcription	HSMM	muscle
37	chr16:12365200-12378000	Weak transcription	Brain Hippocampus Middle	brain
38	chr16:12365200-12379200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr16:12365200-12382200	Weak transcription	Left Ventricle	heart
40	chr16:12365200-12388000	Weak transcription	Pancreas	Pancrea
41	chr16:12365200-12388400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr16:12366000-12371800	Weak transcription	NHEK	skin
43	chr16:12366400-12384000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr16:12366600-12370800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr16:12368600-12369400	Enhancers	HepG2	liver

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