Variant report

Variant	rs1986424
Chromosome Location	chr1:222058995-222058996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221915372..221918031-chr1:222058617..222062321,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11808477	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811613	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846733	0.86[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	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1986424	USH2A	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222048600-222073600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:222048800-222060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:222052400-222059400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:222053000-222059200	Weak transcription	HMEC	breast
5	chr1:222053000-222059600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:222053000-222059600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:222053000-222060200	Weak transcription	HSMMtube	muscle
8	chr1:222053000-222060400	Weak transcription	Aorta	Aorta
9	chr1:222054200-222059400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:222054600-222059400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:222055000-222059400	Weak transcription	Adipose Nuclei	Adipose
12	chr1:222055400-222059800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:222055400-222060400	Weak transcription	Ovary	ovary
14	chr1:222055800-222059400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:222056000-222059400	Weak transcription	NHDF-Ad	bronchial
16	chr1:222056000-222059600	Weak transcription	Osteobl	bone
17	chr1:222057400-222060400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:222057800-222059000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:222057800-222060400	Enhancers	Hela-S3	cervix
20	chr1:222058400-222059000	Enhancers	HSMM	muscle
21	chr1:222058400-222059400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:222058600-222059400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:222058600-222059600	Weak transcription	Psoas Muscle	Psoas
24	chr1:222058600-222060000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:222058600-222060400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:222058600-222061400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:222058800-222060400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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