Variant report

Variant	rs353407
Chromosome Location	chr19:38444944-38444945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38441551..38443321-chr19:38443505..38445243,2	K562	blood:
2	chr19:38432664..38434680-chr19:38442017..38444946,2	MCF-7	breast:
3	chr19:38443941..38445562-chr19:38447183..38449175,2	MCF-7	breast:
4	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];0.97[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]
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]
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
rs353407	PAFAH1B3	cis	cerebellum	SCAN
rs353407	PHLDB3	cis	parietal	SCAN
rs353407	CBLC	cis	parietal	SCAN
rs353407	DMPK	cis	parietal	SCAN
rs353407	AXL	cis	cerebellum	SCAN
rs353407	WDR87	cis	Thyroid	GTEx
rs353407	PHLDB3	cis	cerebellum	SCAN
rs353407	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 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	chr19:38439000-38445200	Weak transcription	Fetal Heart	heart
9	chr19:38439600-38453000	Weak transcription	Gastric	stomach
10	chr19:38440000-38446400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:38440800-38449600	Enhancers	Primary B cells from cord blood	blood
12	chr19:38441000-38445200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr19:38441000-38446600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:38441600-38445200	Enhancers	Osteobl	bone
16	chr19:38441600-38449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:38441800-38445600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:38442000-38445000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:38442000-38445600	Enhancers	GM12878-XiMat	blood
20	chr19:38442000-38445800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:38442200-38445000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:38442400-38445200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:38442400-38445400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr19:38442600-38445200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:38442800-38445200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr19:38443000-38447800	Weak transcription	Stomach Mucosa	stomach
27	chr19:38443200-38445200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr19:38443400-38445200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:38443400-38445400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr19:38443400-38445400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:38443400-38445600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:38443600-38445200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr19:38443600-38445200	Enhancers	NH-A	brain
34	chr19:38443600-38445800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:38443800-38445000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:38443800-38445000	Weak transcription	Lung	lung
37	chr19:38443800-38445200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:38443800-38445200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:38443800-38445200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:38443800-38445200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr19:38443800-38445400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr19:38443800-38445400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr19:38443800-38445400	Enhancers	Fetal Kidney	kidney
44	chr19:38443800-38445600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr19:38443800-38445600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:38443800-38445600	Enhancers	Fetal Intestine Large	intestine
47	chr19:38444000-38445000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:38444000-38445200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:38444000-38445200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr19:38444000-38445200	Enhancers	Duodenum Mucosa	Duodenum

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