Variant report

Variant	rs8019328
Chromosome Location	chr14:39890545-39890546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39882950..39886541-chr14:39887581..39892204,4	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10143351	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10145949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872920	0.81[ASW][hapmap]
rs11157053	0.81[ASW][hapmap]
rs11621330	0.81[ASW][hapmap]
rs12883652	0.85[AFR][1000 genomes]
rs12893829	0.89[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs1955703	0.86[ASN][1000 genomes]
rs2038278	0.83[AFR][1000 genomes]
rs2415543	0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs2415545	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902558	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs4902560	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs6571923	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6571932	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7142748	0.86[ASN][1000 genomes]
rs7148377	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs7160664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718364	0.93[ASW][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs8006893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8011173	0.87[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8012768	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8019328	CTAGE5	cis	multi-tissue	Pritchard
rs8019328	PPP2R3C	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39863400-39891600	Weak transcription	Small Intestine	intestine
2	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:39865000-39891200	Weak transcription	Psoas Muscle	Psoas
4	chr14:39865000-39898200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:39869000-39895600	Weak transcription	Hela-S3	cervix
6	chr14:39882200-39895400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr14:39885200-39891400	Weak transcription	Gastric	stomach
8	chr14:39886000-39890800	Weak transcription	Fetal Brain Male	brain
9	chr14:39886000-39895600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:39886200-39890600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:39886200-39895600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr14:39886400-39892600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr14:39886400-39895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:39886600-39890800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:39886600-39890800	Weak transcription	Brain Angular Gyrus	brain
16	chr14:39886600-39891200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:39886600-39891200	Weak transcription	Lung	lung
18	chr14:39886600-39891200	Weak transcription	Ovary	ovary
19	chr14:39886600-39891200	Weak transcription	Right Ventricle	heart
20	chr14:39886600-39891400	Weak transcription	Aorta	Aorta
21	chr14:39886600-39891800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr14:39886600-39894000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr14:39886600-39894400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr14:39886600-39895600	Weak transcription	Fetal Lung	lung
25	chr14:39886600-39895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr14:39886600-39895800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr14:39886600-39898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
29	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
30	chr14:39886800-39891200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr14:39886800-39892600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr14:39886800-39895600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr14:39886800-39895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr14:39886800-39895600	Weak transcription	HepG2	liver
35	chr14:39886800-39895800	Weak transcription	Brain Anterior Caudate	brain
36	chr14:39886800-39895800	Weak transcription	Fetal Thymus	thymus
37	chr14:39886800-39895800	Weak transcription	Thymus	Thymus
38	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr14:39887000-39895800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr14:39887000-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr14:39887200-39895400	Weak transcription	Dnd41	blood
43	chr14:39887200-39895600	Weak transcription	GM12878-XiMat	blood
44	chr14:39887600-39891200	Weak transcription	Fetal Intestine Small	intestine
45	chr14:39887600-39898000	Weak transcription	Fetal Stomach	stomach
46	chr14:39888200-39890800	Strong transcription	Primary B cells from cord blood	blood
47	chr14:39888800-39891600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:39889000-39890800	Weak transcription	Fetal Heart	heart
49	chr14:39889200-39892600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:39889400-39891600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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