Variant report

Variant	rs353402
Chromosome Location	chr19:38446088-38446089
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	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap]
rs1119229	0.88[CEU][hapmap]
rs1643462	0.95[EUR][1000 genomes]
rs1643463	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643466	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1643467	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs1643468	1.00[CEU][hapmap];0.84[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];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]
rs1725499	0.88[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs241932	1.00[CEU][hapmap];0.96[TSI][hapmap]
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]
rs353399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353400	0.98[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]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs353415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];0.86[YRI][hapmap];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]
rs3786869	0.87[CEU][hapmap]
rs4239516	0.87[CEU][hapmap]
rs4803524	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap]
rs4803551	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs4803573	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs705491	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs705492	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs705493	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs705494	1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs705495	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs705500	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7250409	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7258597	0.89[EUR][1000 genomes]
rs752878	0.95[EUR][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap]
rs8107341	1.00[EUR][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs8112706	1.00[CEU][hapmap]
rs8113521	0.88[CEU][hapmap]
rs833895	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs833896	0.94[EUR][1000 genomes]
rs833897	0.95[EUR][1000 genomes]
rs833898	0.95[EUR][1000 genomes]
rs833914	0.80[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs833926	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs856299	0.80[JPT][hapmap]
rs856300	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs856304	1.00[CEU][hapmap];0.92[TSI][hapmap]
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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs353402	CBLC	cis	parietal	SCAN
rs353402	DMPK	cis	parietal	SCAN
rs353402	PHLDB3	cis	parietal	SCAN
rs353402	PAFAH1B3	cis	cerebellum	SCAN
rs353402	WDR87	cis	Thyroid	GTEx
rs353402	PHLDB3	cis	cerebellum	SCAN
rs353402	ZNF571	cis	multi-tissue	Pritchard
rs353402	AXL	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr19:38440000-38446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
11	chr19:38441000-38446600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:38443000-38447800	Weak transcription	Stomach Mucosa	stomach
15	chr19:38444000-38446400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38444000-38453200	Weak transcription	Pancreas	Pancrea
17	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:38444400-38446600	Weak transcription	Psoas Muscle	Psoas
19	chr19:38444600-38446200	Weak transcription	NHEK	skin
20	chr19:38444600-38446400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:38444600-38446400	Weak transcription	HMEC	breast
22	chr19:38444600-38446600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:38444600-38450000	Weak transcription	NHDF-Ad	bronchial
24	chr19:38444600-38453600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
26	chr19:38445200-38446200	Weak transcription	Brain Anterior Caudate	brain
27	chr19:38445200-38446400	Enhancers	Fetal Heart	heart
28	chr19:38445200-38446600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:38445200-38449600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr19:38445200-38449800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr19:38445200-38450000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:38445200-38450000	Weak transcription	Osteobl	bone
33	chr19:38445200-38450600	Weak transcription	HSMM	muscle
34	chr19:38445200-38452000	Weak transcription	NH-A	brain
35	chr19:38445200-38453200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:38445200-38453200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:38445200-38456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:38445200-38456400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:38445400-38446200	Weak transcription	A549	lung
40	chr19:38445400-38446400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:38445400-38448200	Weak transcription	Fetal Intestine Small	intestine
42	chr19:38445400-38450200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:38445600-38446200	Weak transcription	GM12878-XiMat	blood
45	chr19:38445600-38446600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:38445600-38446800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:38445600-38450000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:38445600-38451800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:38445600-38453200	Weak transcription	Fetal Intestine Large	intestine
50	chr19:38445800-38446200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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