Variant report

Variant	rs56226439
Chromosome Location	chr5:14242621-14242622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14217173..14219209-chr5:14242160..14244276,2	MCF-7	breast:
2	chr5:14190314..14192078-chr5:14242022..14244161,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12522960	0.81[ASN][1000 genomes]
rs12659261	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs154150	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16903326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16903338	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30603	0.95[EUR][1000 genomes]
rs30604	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs30605	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30618	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42204	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67084079	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72744279	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7380307	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7700787	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14221800-14249600	Weak transcription	Colonic Mucosa	Colon
2	chr5:14226400-14249400	Weak transcription	Esophagus	oesophagus
3	chr5:14226600-14246800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:14234600-14250200	Weak transcription	Placenta	Placenta
5	chr5:14237800-14244000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:14237800-14246600	Weak transcription	Pancreas	Pancrea
7	chr5:14238000-14250000	Weak transcription	HepG2	liver
8	chr5:14238000-14252400	Weak transcription	NHEK	skin
9	chr5:14238400-14246800	Weak transcription	Hela-S3	cervix
10	chr5:14238400-14249400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:14238400-14249600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:14238600-14242800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:14238600-14243000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:14238600-14243000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:14238600-14244000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:14238600-14244000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:14238600-14244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:14238600-14244000	Weak transcription	Thymus	Thymus
19	chr5:14238600-14247000	Weak transcription	HMEC	breast
20	chr5:14238600-14250200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:14238800-14243000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:14238800-14243000	Weak transcription	Spleen	Spleen
23	chr5:14238800-14243200	Weak transcription	Fetal Thymus	thymus
24	chr5:14238800-14244800	Weak transcription	Brain Anterior Caudate	brain
25	chr5:14239800-14242800	Enhancers	Brain Germinal Matrix	brain
26	chr5:14239800-14244800	Weak transcription	Gastric	stomach
27	chr5:14240000-14243000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:14240000-14244000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:14240000-14244800	Enhancers	HSMMtube	muscle
30	chr5:14240000-14247000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:14240000-14249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:14240200-14248600	Weak transcription	Aorta	Aorta
33	chr5:14240400-14243400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:14240400-14246200	Weak transcription	Primary B cells from cord blood	blood
35	chr5:14240600-14243000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:14240600-14243200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:14240600-14243400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:14240600-14243400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:14240800-14242800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:14240800-14242800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:14240800-14242800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:14240800-14242800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:14240800-14242800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:14240800-14243000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr5:14240800-14243200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:14240800-14244800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:14240800-14245000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:14240800-14246400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr5:14240800-14247000	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:14240800-14248800	Weak transcription	Primary B cells from peripheral blood	blood

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