Variant report

Variant	rs353399
Chromosome Location	chr19:38446675-38446676
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	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10404567	0.89[EUR][1000 genomes]
rs1643462	0.95[EUR][1000 genomes]
rs1643463	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643466	0.95[EUR][1000 genomes]
rs1643467	0.95[EUR][1000 genomes]
rs1643468	0.95[EUR][1000 genomes]
rs1643469	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725477	0.95[EUR][1000 genomes]
rs1725478	0.95[EUR][1000 genomes]
rs1725480	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725481	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725482	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725483	0.95[EUR][1000 genomes]
rs1725485	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725487	0.95[EUR][1000 genomes]
rs1725488	0.94[EUR][1000 genomes]
rs1725494	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544718	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35209753	0.87[EUR][1000 genomes]
rs353398	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353403	0.98[EUR][1000 genomes]
rs353404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353414	1.00[EUR][1000 genomes]
rs353415	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs353416	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353417	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353419	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353420	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353421	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353423	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353425	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353428	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353429	0.93[EUR][1000 genomes]
rs353430	0.97[EUR][1000 genomes]
rs705492	1.00[EUR][1000 genomes]
rs705494	0.91[EUR][1000 genomes]
rs705500	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7250409	0.91[EUR][1000 genomes]
rs7258597	0.89[EUR][1000 genomes]
rs752878	0.95[EUR][1000 genomes]
rs8107341	1.00[EUR][1000 genomes]
rs8110284	0.90[EUR][1000 genomes]
rs833895	0.93[EUR][1000 genomes]
rs833896	0.94[EUR][1000 genomes]
rs833897	0.95[EUR][1000 genomes]
rs833898	0.95[EUR][1000 genomes]
rs833926	1.00[EUR][1000 genomes]
rs9304572	0.91[EUR][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs353399	ZNF571	cis	multi-tissue	Pritchard
rs353399	WDR87	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
2	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:38426600-38450800	Weak transcription	Ovary	ovary
4	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
5	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
6	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
7	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:38439600-38453000	Weak transcription	Gastric	stomach
9	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
10	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:38443000-38447800	Weak transcription	Stomach Mucosa	stomach
13	chr19:38444000-38453200	Weak transcription	Pancreas	Pancrea
14	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38444600-38450000	Weak transcription	NHDF-Ad	bronchial
16	chr19:38444600-38453600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
18	chr19:38445200-38449600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:38445200-38449800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:38445200-38450000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:38445200-38450000	Weak transcription	Osteobl	bone
22	chr19:38445200-38450600	Weak transcription	HSMM	muscle
23	chr19:38445200-38452000	Weak transcription	NH-A	brain
24	chr19:38445200-38453200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:38445200-38453200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:38445200-38456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:38445200-38456400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr19:38445400-38448200	Weak transcription	Fetal Intestine Small	intestine
29	chr19:38445400-38450200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:38445600-38446800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:38445600-38450000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr19:38445600-38451800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:38445600-38453200	Weak transcription	Fetal Intestine Large	intestine
35	chr19:38445800-38448400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:38446200-38446800	Enhancers	NHEK	skin
37	chr19:38446200-38447000	ZNF genes & repeats	GM12878-XiMat	blood
38	chr19:38446200-38448000	Genic enhancers	A549	lung
39	chr19:38446400-38447000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:38446400-38447000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:38446400-38447000	Enhancers	HMEC	breast
42	chr19:38446400-38448800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:38446400-38456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:38446600-38446800	Enhancers	H9 Cell Line	embryonic stem cell
45	chr19:38446600-38446800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:38446600-38446800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:38446600-38446800	Enhancers	Psoas Muscle	Psoas
48	chr19:38446600-38447000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr19:38446600-38447000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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