Variant report

Variant	rs72786354
Chromosome Location	chr5:90602209-90602210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90596993..90603089-chr5:90675309..90679333,6	MCF-7	breast:
2	chr5:90600132..90605007-chr5:90674988..90680589,6	K562	blood:
3	chr5:90600628..90605200-chr5:90606247..90608761,5	K562	blood:
4	chr5:90600532..90604276-chr5:90606355..90609607,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARRDC3-1	chr5:90599690-90606849	XLOC_004924
2	lnc-ARRDC3-1	chr5:90601497-90608312	NONHSAT102743

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction
ENSG00000248323	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10474341	0.82[ASN][1000 genomes]
rs12188638	0.82[ASN][1000 genomes]
rs12514996	1.00[AFR][1000 genomes]
rs12520306	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12521670	1.00[AFR][1000 genomes]
rs12653995	0.86[ASN][1000 genomes]
rs12658394	0.93[EUR][1000 genomes]
rs12658748	1.00[AFR][1000 genomes]
rs16869618	0.82[ASN][1000 genomes]
rs2175437	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28369128	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34107416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56316727	0.90[ASN][1000 genomes]
rs56377435	0.90[ASN][1000 genomes]
rs56876862	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57859727	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58781250	1.00[ASN][1000 genomes]
rs61156097	1.00[AFR][1000 genomes]
rs67220802	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67863612	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6888057	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72786311	0.82[ASN][1000 genomes]
rs72786318	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72786321	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72786324	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72786325	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72786326	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72786329	0.86[ASN][1000 genomes]
rs72786331	0.90[ASN][1000 genomes]
rs72786332	0.90[ASN][1000 genomes]
rs72786338	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72786350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72786353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72786359	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72786360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647558	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90589800-90607400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:90593000-90602400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:90593000-90606400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:90593000-90607000	Weak transcription	Left Ventricle	heart
5	chr5:90593000-90607000	Weak transcription	HSMMtube	muscle
6	chr5:90597800-90602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:90598000-90602600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:90598000-90602600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:90598000-90606800	Weak transcription	Adipose Nuclei	Adipose
10	chr5:90598000-90607000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:90598400-90602400	Weak transcription	Right Atrium	heart
12	chr5:90598400-90603600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr5:90598400-90606000	Weak transcription	Primary B cells from cord blood	blood
14	chr5:90599000-90607200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:90600400-90607000	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:90600800-90607200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:90601200-90602600	Enhancers	Psoas Muscle	Psoas
18	chr5:90601200-90603200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr5:90601200-90603600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:90601200-90603800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:90601400-90603200	Strong transcription	A549	lung
22	chr5:90601400-90604600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:90601600-90602600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:90601600-90603000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr5:90601600-90603000	Enhancers	Hela-S3	cervix
26	chr5:90601800-90602600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:90601800-90603200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:90601800-90603400	Enhancers	NHEK	skin
29	chr5:90601800-90603800	Enhancers	HMEC	breast
30	chr5:90601800-90607000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:90602000-90602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:90602000-90603600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr5:90602000-90604200	Enhancers	NHDF-Ad	bronchial
34	chr5:90602200-90603000	Enhancers	Rectal Smooth Muscle	rectum
35	chr5:90602200-90603200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:90602200-90603400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:90602200-90604000	Enhancers	Osteobl	bone
38	chr5:90602200-90607200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:90602200-90607200	Weak transcription	Brain Substantia Nigra	brain

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