Variant report

Variant	rs521538
Chromosome Location	chr1:94525623-94525624
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	chr1:94524835..94527724-chr1:94798552..94800345,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226835	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1191228	0.82[EUR][1000 genomes]
rs17110929	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs539435	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs553608	0.95[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][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	nsv871172	chr1:94504545-94535546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv871057	chr1:94513142-94577286	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs521538	ARHGAP29	cis	parietal	SCAN
rs521538	ABCA4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94515800-94527200	Weak transcription	Spleen	Spleen
2	chr1:94517200-94526800	Weak transcription	A549	lung
3	chr1:94517200-94527200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94521000-94534400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94521400-94527200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:94521600-94526600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:94521600-94527000	Weak transcription	NH-A	brain
8	chr1:94521800-94527000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:94522000-94527000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:94522000-94527200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:94522200-94526800	Weak transcription	HMEC	breast
12	chr1:94522200-94527200	Weak transcription	NHEK	skin
13	chr1:94522200-94533800	Weak transcription	Aorta	Aorta
14	chr1:94522400-94525800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:94522400-94526800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:94522400-94526800	Weak transcription	HSMM	muscle
17	chr1:94522400-94526800	Weak transcription	HSMMtube	muscle
18	chr1:94522400-94526800	Weak transcription	NHDF-Ad	bronchial
19	chr1:94522400-94527200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:94522600-94527000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:94522600-94528600	Weak transcription	Fetal Lung	lung
22	chr1:94522600-94533200	Weak transcription	Gastric	stomach
23	chr1:94522800-94527000	Weak transcription	Osteobl	bone
24	chr1:94522800-94533400	Weak transcription	Stomach Mucosa	stomach
25	chr1:94523000-94527000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:94523200-94533600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:94523600-94530400	Enhancers	Left Ventricle	heart
28	chr1:94523800-94527200	Weak transcription	Psoas Muscle	Psoas
29	chr1:94524200-94526600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:94524200-94527600	Weak transcription	Lung	lung
31	chr1:94524400-94527800	Enhancers	Right Atrium	heart
32	chr1:94524600-94531200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:94525000-94526000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:94525000-94526000	Weak transcription	HUVEC	blood vessel
35	chr1:94525000-94530600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:94525200-94527200	Weak transcription	Right Ventricle	heart
37	chr1:94525200-94529600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:94525400-94526600	Weak transcription	Adipose Nuclei	Adipose
39	chr1:94525400-94527200	Enhancers	HepG2	liver

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