Variant report

Variant	rs1980062
Chromosome Location	chr1:150509169-150509170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150503131..150505095-chr1:150506786..150509617,2	MCF-7	breast:
2	chr1:150507836..150509751-chr1:150550511..150552125,2	MCF-7	breast:
3	chr1:150507220..150509372-chr1:150523215..150524726,2	MCF-7	breast:
4	chr1:150207127..150208912-chr1:150507485..150510087,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAMTSL4-1	chr1:150508143-150509639	XLOC_000403
2	lnc-ADAMTSL4-1	chr1:150508143-150509813	XLOC_000403

No data

Variant related genes	Relation type
ENSG00000143382	Chromatin interaction
ENSG00000264553	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11205386	0.85[EUR][1000 genomes]
rs11810419	0.96[ASN][1000 genomes]
rs12129037	0.84[EUR][1000 genomes]
rs12131376	1.00[EUR][1000 genomes]
rs12132918	0.96[EUR][1000 genomes]
rs12134634	1.00[EUR][1000 genomes]
rs34848955	0.96[EUR][1000 genomes]
rs58585637	0.98[ASN][1000 genomes]
rs66464034	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657478	0.98[ASN][1000 genomes]
rs66866430	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72700804	0.92[EUR][1000 genomes]
rs72700806	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72700810	0.96[EUR][1000 genomes]
rs7514515	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150502000-150510800	Weak transcription	Aorta	Aorta
2	chr1:150504200-150511200	Enhancers	Fetal Muscle Trunk	muscle
3	chr1:150504200-150511600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:150504600-150511600	Enhancers	Fetal Muscle Leg	muscle
5	chr1:150505600-150510200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:150505600-150510600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:150505600-150510600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:150505600-150511600	Enhancers	HepG2	liver
9	chr1:150505600-150511800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:150505600-150516000	Weak transcription	Fetal Stomach	stomach
11	chr1:150505600-150516200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:150505600-150521000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:150505800-150510600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:150505800-150510800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:150505800-150511600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr1:150505800-150516000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:150505800-150521000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:150506000-150510000	Weak transcription	Adipose Nuclei	Adipose
19	chr1:150506000-150510400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:150506400-150512000	Enhancers	Placenta	Placenta
21	chr1:150506600-150509600	Weak transcription	K562	blood
22	chr1:150506600-150510000	Weak transcription	Stomach Mucosa	stomach
23	chr1:150506800-150510000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:150506800-150510200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:150506800-150510400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:150506800-150511600	Enhancers	HSMM	muscle
27	chr1:150507000-150510000	Weak transcription	Esophagus	oesophagus
28	chr1:150507000-150510600	Weak transcription	Fetal Intestine Small	intestine
29	chr1:150507200-150511600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:150507400-150511400	Enhancers	NHDF-Ad	bronchial
31	chr1:150507400-150511600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:150507400-150511600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:150507400-150511600	Enhancers	Osteobl	bone
34	chr1:150507800-150509800	Enhancers	NHLF	lung
35	chr1:150508000-150511400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:150508000-150511600	Enhancers	HSMMtube	muscle
37	chr1:150508000-150511800	Enhancers	NH-A	brain
38	chr1:150508200-150509200	Enhancers	Stomach Smooth Muscle	stomach
39	chr1:150508200-150511200	Enhancers	A549	lung
40	chr1:150508200-150511400	Enhancers	Hela-S3	cervix
41	chr1:150508200-150511600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:150508400-150510400	Enhancers	NHEK	skin
43	chr1:150508400-150511200	Enhancers	HMEC	breast
44	chr1:150508400-150511400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:150508400-150511600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:150508600-150511400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:150508800-150509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:150508800-150509800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:150508800-150510000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:150508800-150510000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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