Variant report

Variant	rs245448
Chromosome Location	chr5:14225323-14225324
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14224670..14226292-chr5:14228930..14231358,2	MCF-7	breast:
2	chr5:14143292..14147216-chr5:14223184..14226021,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13184670	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151901	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151902	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164858	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299506	1.00[ASN][1000 genomes]
rs187386	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245451	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245470	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245512	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26057	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26059	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26060	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26061	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27665	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27759	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28010	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32335	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32339	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32341	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32388	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32389	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32390	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32391	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32394	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32395	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354285	1.00[ASN][1000 genomes]
rs354287	0.83[ASN][1000 genomes]
rs354288	1.00[ASN][1000 genomes]
rs354298	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354299	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354301	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354302	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs354310	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354311	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354312	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35594035	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397098	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407517	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424275	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs445553	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533517	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235530	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534466	chr5:13847044-14246208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14216000-14225800	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr5:14216800-14227200	Weak transcription	Hela-S3	cervix
3	chr5:14217000-14234600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:14218400-14230000	Weak transcription	NHEK	skin
5	chr5:14219200-14225400	Weak transcription	Esophagus	oesophagus
6	chr5:14219200-14228800	Enhancers	Fetal Thymus	thymus
7	chr5:14219800-14225400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:14219800-14226000	Weak transcription	Aorta	Aorta
9	chr5:14219800-14226800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:14219800-14227200	Weak transcription	Gastric	stomach
11	chr5:14219800-14229400	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:14219800-14231000	Weak transcription	HMEC	breast
13	chr5:14219800-14231200	Weak transcription	Fetal Stomach	stomach
14	chr5:14220000-14229400	Weak transcription	Brain Angular Gyrus	brain
15	chr5:14220000-14230000	Weak transcription	Fetal Brain Female	brain
16	chr5:14220400-14229400	Weak transcription	Brain Germinal Matrix	brain
17	chr5:14221000-14226000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:14221200-14226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:14221200-14227200	Weak transcription	Fetal Lung	lung
20	chr5:14221400-14227200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:14221400-14227400	Weak transcription	Liver	Liver
22	chr5:14221600-14226800	Weak transcription	NHLF	lung
23	chr5:14221600-14227200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:14221800-14230800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:14221800-14231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:14221800-14249600	Weak transcription	Colonic Mucosa	Colon
27	chr5:14222000-14226800	Enhancers	HUVEC	blood vessel
28	chr5:14222000-14226800	Weak transcription	NHDF-Ad	bronchial
29	chr5:14222600-14226800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:14222600-14228200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:14222600-14228400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:14222800-14225600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:14222800-14225600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:14222800-14227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:14223200-14225600	Weak transcription	Fetal Intestine Small	intestine
36	chr5:14223400-14226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:14223400-14229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:14223400-14230200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:14223600-14225400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:14223600-14225600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:14223600-14226400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:14223600-14227000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:14223600-14229600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:14223600-14230000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:14223800-14225400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:14223800-14225400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:14223800-14225400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:14223800-14225400	Weak transcription	Placenta	Placenta
49	chr5:14223800-14225400	Weak transcription	Lung	lung
50	chr5:14223800-14225400	Weak transcription	Ovary	ovary

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