Variant report

Variant	rs9921728
Chromosome Location	chr16:12353187-12353188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12352461..12354731-chr16:12381586..12384125,2	MCF-7	breast:
2	chr16:12326297..12328332-chr16:12351704..12354773,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11075057	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075058	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075059	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639640	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11644788	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11649626	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11861914	0.81[EUR][1000 genomes]
rs12148953	0.81[EUR][1000 genomes]
rs12445263	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12445569	0.85[EUR][1000 genomes]
rs12446650	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12448443	0.84[EUR][1000 genomes]
rs13335852	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17697005	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17764604	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2089251	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904423	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35818743	0.84[EUR][1000 genomes]
rs4305040	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4780417	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4780418	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4781200	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4781201	0.85[EUR][1000 genomes]
rs4781202	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6498274	0.82[ASN][1000 genomes]
rs7189386	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7189945	0.84[EUR][1000 genomes]
rs7191442	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7192102	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7194718	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7194981	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7195520	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7197417	0.85[EUR][1000 genomes]
rs7199556	0.84[EUR][1000 genomes]
rs7204209	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7204333	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8046012	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8051479	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8058876	0.94[ASN][1000 genomes]
rs8061549	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs868773	0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs869289	0.82[CHB][hapmap]
rs905950	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9284322	0.80[GIH][hapmap]
rs9630612	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921551	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9927705	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9928214	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9930625	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9937220	0.83[EUR][1000 genomes];0.83[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	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	nsv905348	chr16:12299936-12358206	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9921728	CPPED1	cis	cerebellum	SCAN
rs9921728	C16orf63	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12297400-12353800	Weak transcription	Gastric	stomach
2	chr16:12308000-12371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:12309800-12371200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr16:12322600-12353600	Weak transcription	Lung	lung
5	chr16:12323400-12394200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr16:12323800-12373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr16:12330800-12373000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:12333200-12353200	Weak transcription	Spleen	Spleen
9	chr16:12334000-12356600	Weak transcription	Right Atrium	heart
10	chr16:12334400-12356200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:12334600-12371800	Weak transcription	Adipose Nuclei	Adipose
12	chr16:12338200-12356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
14	chr16:12340400-12353800	Weak transcription	Pancreas	Pancrea
15	chr16:12340800-12353200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:12346800-12356200	Weak transcription	Fetal Brain Male	brain
17	chr16:12347200-12356200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr16:12347800-12356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
20	chr16:12348200-12371400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:12348800-12354200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr16:12349800-12353200	Strong transcription	Primary T cells from cord blood	blood
23	chr16:12349800-12354800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr16:12350000-12354600	Enhancers	Fetal Muscle Leg	muscle
25	chr16:12350200-12354400	Enhancers	Fetal Muscle Trunk	muscle
26	chr16:12350200-12371600	Weak transcription	GM12878-XiMat	blood
27	chr16:12350600-12354800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:12350800-12354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr16:12351000-12353800	Enhancers	Brain Angular Gyrus	brain
30	chr16:12351000-12354400	Enhancers	Brain Cingulate Gyrus	brain
31	chr16:12351200-12353600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:12351200-12353800	Weak transcription	Esophagus	oesophagus
33	chr16:12351200-12373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr16:12351200-12382800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:12351400-12356000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr16:12351600-12353200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr16:12351600-12353800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:12351800-12353400	Enhancers	Brain Hippocampus Middle	brain
39	chr16:12351800-12354200	Enhancers	Brain Anterior Caudate	brain
40	chr16:12352000-12354200	Weak transcription	Fetal Intestine Large	intestine
41	chr16:12352000-12354400	Enhancers	Ovary	ovary
42	chr16:12352000-12355400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr16:12352200-12353200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:12352200-12353800	Weak transcription	Fetal Heart	heart
45	chr16:12352200-12354000	Weak transcription	Liver	Liver
46	chr16:12352200-12354000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr16:12352400-12354000	Enhancers	HepG2	liver
48	chr16:12352400-12354600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr16:12352600-12353200	Enhancers	Brain Germinal Matrix	brain
50	chr16:12352600-12354000	Enhancers	Brain Substantia Nigra	brain

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