Variant report

Variant	rs1725469
Chromosome Location	chr19:38472593-38472594
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:
2	chr19:38421146..38425969-chr19:38469812..38473788,8	MCF-7	breast:
3	chr19:38471726..38473895-chr19:38475514..38478507,2	MCF-7	breast:
4	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
5	chr19:38417337..38419728-chr19:38472151..38473762,2	MCF-7	breast:
6	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
7	chr19:38464299..38466897-chr19:38471672..38473805,2	MCF-7	breast:
8	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:
9	chr19:38394269..38398486-chr19:38470778..38473091,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1643462	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1643463	0.80[EUR][1000 genomes]
rs1643466	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1643467	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1643468	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725477	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725478	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725480	0.80[EUR][1000 genomes]
rs1725481	0.80[EUR][1000 genomes]
rs1725482	0.80[EUR][1000 genomes]
rs1725483	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725485	0.80[EUR][1000 genomes]
rs1725487	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725488	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353398	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs353403	0.81[ASN][1000 genomes]
rs353414	0.91[ASN][1000 genomes]
rs353420	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs353423	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs353425	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs353429	0.80[ASN][1000 genomes]
rs353430	0.86[ASN][1000 genomes]
rs705492	0.82[ASN][1000 genomes]
rs705500	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs752878	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs833895	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833896	0.87[ASN][1000 genomes]
rs833897	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833898	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833914	0.92[AFR][1000 genomes];0.92[ASN][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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
8	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:38468200-38473600	Enhancers	Lung	lung
10	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:38468200-38475600	Enhancers	HMEC	breast
13	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:38468400-38473000	Enhancers	NH-A	brain
16	chr19:38468400-38473200	Enhancers	HSMM	muscle
17	chr19:38468800-38474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
19	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
22	chr19:38470000-38472800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr19:38470200-38472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:38470200-38473200	Enhancers	Fetal Lung	lung
25	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
27	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr19:38470400-38472600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr19:38470400-38473600	Enhancers	Pancreas	Pancrea
30	chr19:38470400-38474400	Enhancers	Esophagus	oesophagus
31	chr19:38470400-38474800	Enhancers	Gastric	stomach
32	chr19:38470600-38472600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:38470600-38473200	Enhancers	HSMMtube	muscle
34	chr19:38470600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:38470800-38472600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:38470800-38473000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:38470800-38473600	Enhancers	Small Intestine	intestine
38	chr19:38470800-38474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr19:38470800-38477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
41	chr19:38471000-38472800	Enhancers	Fetal Kidney	kidney
42	chr19:38471000-38475400	Enhancers	NHEK	skin
43	chr19:38471000-38476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:38471200-38472800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr19:38471200-38474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr19:38471400-38473400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:38471400-38473400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:38471400-38473800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:38471400-38476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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