Variant report

Variant	rs56235530
Chromosome Location	chr5:14227009-14227010
allele	-/TTGCAGCTCTCCTCCTCC
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14143875..14146353-chr5:14226756..14228608,4	MCF-7	breast:
2	chr5:14219689..14221561-chr5:14226743..14228313,2	K562	blood:
3	chr5:14220578..14224492-chr5:14225553..14229108,5	MCF-7	breast:
4	chr5:14143211..14145385-chr5:14226496..14228720,2	K562	blood:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13184670	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151901	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151902	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164858	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299506	1.00[ASN][1000 genomes]
rs187386	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245447	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245448	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245451	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs245470	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245512	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26057	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26059	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26060	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26061	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27665	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27759	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28010	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32335	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32339	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32341	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32388	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32389	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32390	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32391	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32394	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32395	0.85[AMR][1000 genomes];0.99[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	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354299	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354300	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354301	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354302	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs354310	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354311	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354312	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35594035	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397098	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407517	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424275	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs445553	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533517	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv4724	chr5:14225543-14243167	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14216800-14227200	Weak transcription	Hela-S3	cervix
2	chr5:14217000-14234600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:14218400-14230000	Weak transcription	NHEK	skin
4	chr5:14219200-14228800	Enhancers	Fetal Thymus	thymus
5	chr5:14219800-14227200	Weak transcription	Gastric	stomach
6	chr5:14219800-14229400	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:14219800-14231000	Weak transcription	HMEC	breast
8	chr5:14219800-14231200	Weak transcription	Fetal Stomach	stomach
9	chr5:14220000-14229400	Weak transcription	Brain Angular Gyrus	brain
10	chr5:14220000-14230000	Weak transcription	Fetal Brain Female	brain
11	chr5:14220400-14229400	Weak transcription	Brain Germinal Matrix	brain
12	chr5:14221200-14227200	Weak transcription	Fetal Lung	lung
13	chr5:14221400-14227200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:14221400-14227400	Weak transcription	Liver	Liver
15	chr5:14221600-14227200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:14221800-14230800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:14221800-14231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:14221800-14249600	Weak transcription	Colonic Mucosa	Colon
19	chr5:14222600-14228200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:14222600-14228400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:14222800-14227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:14223400-14229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:14223400-14230200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:14223600-14229600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:14223600-14230000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:14223800-14227200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:14223800-14229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:14223800-14230400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:14223800-14237600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:14224000-14228000	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:14224000-14231400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:14224000-14237400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:14224000-14239600	Weak transcription	Primary B cells from cord blood	blood
34	chr5:14224600-14228000	Enhancers	A549	lung
35	chr5:14225000-14227600	Enhancers	Left Ventricle	heart
36	chr5:14225000-14228800	Enhancers	Right Ventricle	heart
37	chr5:14225000-14230000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:14225000-14237600	Genic enhancers	HSMM	muscle
39	chr5:14225200-14227400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:14225200-14227800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:14225200-14228000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr5:14225400-14227400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:14225400-14227400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:14225400-14227400	Enhancers	Lung	lung
45	chr5:14225400-14228600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr5:14225400-14228800	Enhancers	Placenta	Placenta
47	chr5:14225400-14230600	Enhancers	Ovary	ovary
48	chr5:14225600-14227400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:14225600-14227400	Enhancers	Fetal Muscle Trunk	muscle
50	chr5:14225600-14227600	Enhancers	Pancreas	Pancrea

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