Variant report

Variant	rs2544718
Chromosome Location	chr19:38456017-38456018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
2	chr19:38455932..38458635-chr19:38458979..38461344,2	MCF-7	breast:
3	chr19:38395370..38399266-chr19:38452571..38456602,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10404567	0.86[EUR][1000 genomes]
rs1643462	0.92[EUR][1000 genomes]
rs1643463	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1643466	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1643467	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1643468	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1643469	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725477	0.92[EUR][1000 genomes]
rs1725478	0.92[EUR][1000 genomes]
rs1725480	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725481	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725482	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725483	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1725485	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725487	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1725488	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1725494	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35209753	0.85[EUR][1000 genomes]
rs353398	0.97[EUR][1000 genomes]
rs353399	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353400	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353402	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353403	0.95[EUR][1000 genomes]
rs353404	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353407	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353414	0.97[EUR][1000 genomes]
rs353415	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353416	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353417	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353419	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353420	0.97[EUR][1000 genomes]
rs353421	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353423	0.97[EUR][1000 genomes]
rs353424	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353425	0.97[EUR][1000 genomes]
rs353426	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353427	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353428	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353429	0.90[EUR][1000 genomes]
rs353430	0.94[EUR][1000 genomes]
rs705492	0.97[EUR][1000 genomes]
rs705494	0.88[EUR][1000 genomes]
rs705500	0.97[EUR][1000 genomes]
rs7250409	0.88[EUR][1000 genomes]
rs7258597	0.86[EUR][1000 genomes]
rs752878	0.92[EUR][1000 genomes]
rs8107341	0.97[EUR][1000 genomes]
rs8110284	0.87[EUR][1000 genomes]
rs833895	0.90[EUR][1000 genomes]
rs833896	0.92[EUR][1000 genomes]
rs833897	0.92[EUR][1000 genomes]
rs833898	0.92[EUR][1000 genomes]
rs833926	0.97[EUR][1000 genomes]
rs9304572	0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2544718	WDR87	cis	Thyroid	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
3	chr19:38445200-38456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:38445200-38456400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:38446400-38456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:38449800-38456800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:38452400-38456600	Weak transcription	Primary T cells from cord blood	blood
9	chr19:38452800-38456400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:38453000-38456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:38453200-38457800	Genic enhancers	A549	lung
12	chr19:38453400-38456800	Weak transcription	Esophagus	oesophagus
13	chr19:38453400-38456800	Enhancers	HSMM	muscle
14	chr19:38454000-38458000	Weak transcription	Small Intestine	intestine
15	chr19:38454200-38456400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:38454200-38456400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:38454200-38456400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:38454200-38456400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr19:38454200-38456800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38454200-38456800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr19:38454200-38456800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:38454200-38456800	Weak transcription	Gastric	stomach
23	chr19:38454200-38456800	Weak transcription	Pancreas	Pancrea
24	chr19:38454200-38456800	Weak transcription	Spleen	Spleen
25	chr19:38454200-38456800	Weak transcription	HepG2	liver
26	chr19:38454200-38457200	Weak transcription	Lung	lung
27	chr19:38454400-38456600	Weak transcription	HMEC	breast
28	chr19:38454400-38456800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr19:38454400-38457000	Weak transcription	Stomach Mucosa	stomach
30	chr19:38454400-38460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:38454400-38461200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:38454600-38460800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr19:38454600-38461000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:38454800-38456400	Weak transcription	Fetal Intestine Small	intestine
35	chr19:38454800-38457000	Weak transcription	NHDF-Ad	bronchial
36	chr19:38454800-38459200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr19:38454800-38459200	Weak transcription	NHLF	lung
38	chr19:38455000-38456200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr19:38455000-38456400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:38455000-38456400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:38455000-38456400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:38455000-38456400	Weak transcription	HSMMtube	muscle
43	chr19:38455000-38456400	Weak transcription	NH-A	brain
44	chr19:38455000-38456600	Weak transcription	Fetal Intestine Large	intestine
45	chr19:38455000-38456800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr19:38455000-38456800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:38455000-38457000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:38455200-38457000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:38455200-38459400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:38455200-38461400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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