Variant report

Variant	rs1643469
Chromosome Location	chr19:38457809-38457810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38457253..38459371-chr19:38481407..38483076,2	MCF-7	breast:
2	chr19:38455932..38458635-chr19:38458979..38461344,2	MCF-7	breast:
3	chr19:38395796..38398301-chr19:38456658..38458907,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10404567	0.87[EUR][1000 genomes]
rs1643462	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1643463	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1643466	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1643467	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1643468	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725477	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725478	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725480	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725481	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725482	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725483	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725485	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725487	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725488	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1725494	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2544718	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35209753	0.86[EUR][1000 genomes]
rs353398	0.98[EUR][1000 genomes]
rs353399	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353400	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353402	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353403	0.96[EUR][1000 genomes]
rs353404	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353407	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353414	0.98[EUR][1000 genomes]
rs353415	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353416	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353417	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353419	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353420	0.98[EUR][1000 genomes]
rs353421	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353423	0.98[EUR][1000 genomes]
rs353424	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353425	0.98[EUR][1000 genomes]
rs353426	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353427	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353428	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353429	0.91[EUR][1000 genomes]
rs353430	0.95[EUR][1000 genomes]
rs705492	0.98[EUR][1000 genomes]
rs705494	0.89[EUR][1000 genomes]
rs705500	0.98[EUR][1000 genomes]
rs7250409	0.89[EUR][1000 genomes]
rs7258597	0.87[EUR][1000 genomes]
rs752878	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs8107341	0.98[EUR][1000 genomes]
rs8110284	0.88[EUR][1000 genomes]
rs833895	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs833896	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs833897	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs833898	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs833926	0.98[EUR][1000 genomes]
rs9304572	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1643469	WDR87	cis	Thyroid	GTEx
rs1643469	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38454000-38458000	Weak transcription	Small Intestine	intestine
2	chr19:38454400-38460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:38454400-38461200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr19:38454600-38460800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr19:38454600-38461000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr19:38454800-38459200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:38454800-38459200	Weak transcription	NHLF	lung
8	chr19:38455200-38459400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:38455200-38461400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr19:38456000-38461000	Weak transcription	Fetal Stomach	stomach
11	chr19:38456200-38459600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:38456400-38458000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38456400-38458200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:38456400-38458400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:38456400-38459200	Genic enhancers	Fetal Intestine Small	intestine
16	chr19:38456600-38458000	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr19:38456600-38458000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:38456600-38458000	Enhancers	Fetal Intestine Large	intestine
19	chr19:38456600-38460800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr19:38456800-38458200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:38456800-38458400	Enhancers	HepG2	liver
22	chr19:38457000-38458000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:38457000-38458400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:38457000-38458400	Enhancers	Osteobl	bone
25	chr19:38457200-38461200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:38457200-38470400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr19:38457400-38458000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:38457400-38459200	Weak transcription	GM12878-XiMat	blood
29	chr19:38457400-38460400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:38457400-38461000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:38457600-38458000	Enhancers	Esophagus	oesophagus
32	chr19:38457600-38458000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr19:38457600-38458600	Enhancers	HMEC	breast
34	chr19:38457600-38459600	Enhancers	HSMM	muscle
35	chr19:38457600-38460400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:38457600-38461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:38457600-38461000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:38457600-38461200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:38457600-38461200	Weak transcription	NHDF-Ad	bronchial
40	chr19:38457600-38470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:38457600-38470400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:38457600-38470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:38457800-38458000	Enhancers	Primary B cells from cord blood	blood
44	chr19:38457800-38458000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:38457800-38458000	Enhancers	NHEK	skin
46	chr19:38457800-38459000	Weak transcription	A549	lung
47	chr19:38457800-38460200	Weak transcription	Primary T cells from cord blood	blood
48	chr19:38457800-38460200	Weak transcription	Stomach Mucosa	stomach
49	chr19:38457800-38461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:38457800-38461000	Weak transcription	Duodenum Mucosa	Duodenum

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