Variant report

Variant	rs4783708
Chromosome Location	chr16:69495181-69495182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69494261..69496702-chr16:69498407..69501487,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10048086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11075720	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153053	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs153058	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs246132	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246138	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs246140	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246142	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246143	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs246144	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246145	0.83[JPT][hapmap]
rs246148	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743670	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499227	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7185800	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206737	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728546	0.83[JPT][hapmap]
rs8064195	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862349	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064808	chr16:69271190-69552951	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv542940	chr16:69271190-69552951	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4783708	LCAT	cis	parietal	SCAN
rs4783708	ZNF23	cis	parietal	SCAN
rs4783708	DYNC1LI2	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69459400-69500600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:69459600-69499000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:69466200-69496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:69473400-69501600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:69473800-69499600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:69478200-69497800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr16:69478400-69496400	Weak transcription	Gastric	stomach
8	chr16:69478400-69498400	Weak transcription	Colonic Mucosa	Colon
9	chr16:69478400-69503200	Weak transcription	Spleen	Spleen
10	chr16:69479000-69497000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr16:69479200-69497600	Weak transcription	Brain Angular Gyrus	brain
12	chr16:69479200-69501400	Weak transcription	Aorta	Aorta
13	chr16:69479400-69497400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:69479400-69497800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr16:69479400-69498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:69479400-69503600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr16:69479600-69517600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:69479800-69505000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:69480600-69497000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr16:69480600-69501200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:69481200-69498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:69481400-69495600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr16:69481400-69503800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr16:69481600-69495600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr16:69481600-69496400	Weak transcription	Lung	lung
26	chr16:69481600-69500800	Weak transcription	Ovary	ovary
27	chr16:69482800-69500800	Weak transcription	Colon Smooth Muscle	Colon
28	chr16:69483000-69496000	Weak transcription	Fetal Brain Male	brain
29	chr16:69483000-69496400	Weak transcription	Fetal Muscle Leg	muscle
30	chr16:69483000-69496400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr16:69483000-69496400	Weak transcription	Thymus	Thymus
32	chr16:69483000-69496400	Strong transcription	Hela-S3	cervix
33	chr16:69483000-69498800	Weak transcription	NHLF	lung
34	chr16:69483000-69499000	Weak transcription	Pancreas	Pancrea
35	chr16:69483000-69501400	Weak transcription	Psoas Muscle	Psoas
36	chr16:69483000-69503600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr16:69483000-69505600	Weak transcription	Right Ventricle	heart
38	chr16:69483200-69497800	Weak transcription	Brain Anterior Caudate	brain
39	chr16:69483400-69496400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr16:69483400-69496400	Weak transcription	HSMMtube	muscle
41	chr16:69483400-69497800	Weak transcription	Fetal Brain Female	brain
42	chr16:69483600-69496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:69483600-69503600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr16:69484000-69497800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr16:69484000-69508200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr16:69484400-69497600	Weak transcription	Brain Hippocampus Middle	brain
47	chr16:69485400-69497400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr16:69485400-69498400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr16:69485400-69498800	Weak transcription	K562	blood
50	chr16:69486400-69496400	Weak transcription	Small Intestine	intestine

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