Variant report

Variant	rs73246657
Chromosome Location	chr5:112619577-112619578
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	chr5:112619318..112622139-chr5:112627969..112630686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10519343	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10519345	0.85[ASN][1000 genomes]
rs10519346	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11241197	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11740045	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11740190	0.83[ASN][1000 genomes]
rs11740233	0.83[ASN][1000 genomes]
rs11740318	0.83[ASN][1000 genomes]
rs11740353	0.83[ASN][1000 genomes]
rs11740443	0.83[ASN][1000 genomes]
rs11741794	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11741937	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11743052	0.83[ASN][1000 genomes]
rs11744606	0.87[ASN][1000 genomes]
rs11746532	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11746791	0.83[ASN][1000 genomes]
rs11746821	0.85[ASN][1000 genomes]
rs11748058	0.85[ASN][1000 genomes]
rs11748465	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11748524	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11749864	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12186466	0.80[ASN][1000 genomes]
rs12188069	0.80[ASN][1000 genomes]
rs12188070	0.80[ASN][1000 genomes]
rs12188230	0.83[ASN][1000 genomes]
rs12518849	0.85[ASN][1000 genomes]
rs12523027	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12523284	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13436236	0.93[EUR][1000 genomes]
rs17135488	0.85[ASN][1000 genomes]
rs17135506	0.85[ASN][1000 genomes]
rs17135507	0.85[ASN][1000 genomes]
rs17135515	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17135517	0.83[ASN][1000 genomes]
rs17135520	0.90[ASN][1000 genomes]
rs17135526	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17135531	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17135534	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17135535	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17135542	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17135543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17135546	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1822488	0.93[EUR][1000 genomes]
rs1845289	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1997521	0.83[ASN][1000 genomes]
rs34271294	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4632792	0.85[ASN][1000 genomes]
rs4705806	0.83[ASN][1000 genomes]
rs4705807	0.85[ASN][1000 genomes]
rs4705808	0.85[ASN][1000 genomes]
rs4705809	0.85[ASN][1000 genomes]
rs4705810	0.83[ASN][1000 genomes]
rs4705811	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56294433	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59107004	0.83[ASN][1000 genomes]
rs59222257	0.83[ASN][1000 genomes]
rs60087454	0.83[ASN][1000 genomes]
rs60437559	0.83[ASN][1000 genomes]
rs6594695	0.83[ASN][1000 genomes]
rs6594696	0.83[ASN][1000 genomes]
rs6594697	0.83[ASN][1000 genomes]
rs66893265	0.83[ASN][1000 genomes]
rs67063423	0.83[ASN][1000 genomes]
rs67373655	0.83[ASN][1000 genomes]
rs67550282	0.83[ASN][1000 genomes]
rs68069850	0.83[ASN][1000 genomes]
rs6879761	0.83[ASN][1000 genomes]
rs6887565	0.87[ASN][1000 genomes]
rs6888602	0.87[ASN][1000 genomes]
rs73244779	0.83[ASN][1000 genomes]
rs73246604	0.85[ASN][1000 genomes]
rs73246629	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73246648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73246677	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73246681	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7724707	0.82[ASN][1000 genomes]
rs7724717	0.82[ASN][1000 genomes]
rs7724936	0.85[ASN][1000 genomes]
rs971370	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs971371	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs971373	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs977997	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112608000-112628200	Weak transcription	HMEC	breast
3	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:112612000-112623800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:112612000-112625200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:112612200-112625200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:112614200-112625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:112615000-112625200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112616600-112620000	Enhancers	Fetal Heart	heart
12	chr5:112616800-112623400	Weak transcription	NHEK	skin
13	chr5:112616800-112623800	Weak transcription	Esophagus	oesophagus
14	chr5:112617000-112619800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr5:112617000-112620400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:112617000-112622000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:112617200-112621200	Weak transcription	Psoas Muscle	Psoas
18	chr5:112617400-112620000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:112617400-112621600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:112617800-112625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:112617800-112628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:112618000-112619600	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr5:112618000-112620000	Enhancers	Brain Cingulate Gyrus	brain
24	chr5:112618200-112623600	Weak transcription	Gastric	stomach
25	chr5:112618400-112620200	Enhancers	Brain Hippocampus Middle	brain
26	chr5:112618400-112621200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:112618400-112621200	Weak transcription	Adipose Nuclei	Adipose
28	chr5:112618400-112628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:112618400-112628200	Weak transcription	Fetal Kidney	kidney
30	chr5:112618400-112628200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:112618400-112628400	Weak transcription	Fetal Stomach	stomach
32	chr5:112618600-112620000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr5:112618600-112620000	Enhancers	Ovary	ovary
34	chr5:112618600-112620200	Enhancers	Brain Substantia Nigra	brain
35	chr5:112618600-112625600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:112618800-112619600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:112618800-112621200	Weak transcription	Right Ventricle	heart
38	chr5:112618800-112622000	Weak transcription	Brain Angular Gyrus	brain
39	chr5:112619000-112619800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:112619000-112621200	Weak transcription	Left Ventricle	heart
41	chr5:112619000-112626800	Weak transcription	Liver	Liver
42	chr5:112619000-112628600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:112619000-112628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:112619200-112619800	Weak transcription	Brain Anterior Caudate	brain
45	chr5:112619200-112625600	Weak transcription	Fetal Lung	lung
46	chr5:112619400-112619600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr5:112619400-112619600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr5:112619400-112619800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:112619400-112620000	Enhancers	Right Atrium	heart
50	chr5:112619400-112621800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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