Variant report

Variant	rs28588542
Chromosome Location	chr3:105180134-105180135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105179946..105182536-chr3:105183412..105185840,2	MCF-7	breast:
2	chr3:105084736..105086274-chr3:105179763..105181298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170017	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12488738	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13080897	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2062434	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2399047	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4541433	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6437595	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7429428	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9819036	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9833101	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843791	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9844458	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863750	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
2	chr3:105167800-105185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:105175200-105184800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:105175400-105184400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105177400-105180200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:105177600-105180600	Enhancers	Brain Substantia Nigra	brain
7	chr3:105177800-105180600	Enhancers	Brain Angular Gyrus	brain
8	chr3:105178000-105180600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:105178200-105180600	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:105179000-105180400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:105179000-105180400	Enhancers	Brain Hippocampus Middle	brain
12	chr3:105179000-105180600	Enhancers	Brain Anterior Caudate	brain
13	chr3:105179000-105185000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:105179000-105191400	Weak transcription	HSMM	muscle
15	chr3:105179000-105192200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:105179200-105182000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:105179200-105184000	Weak transcription	NHDF-Ad	bronchial
18	chr3:105179200-105185600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:105179400-105180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:105179600-105184200	Weak transcription	Liver	Liver
21	chr3:105179600-105184600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:105179600-105192400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:105180000-105180200	Enhancers	Osteobl	bone
24	chr3:105180000-105180400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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