Variant report

Variant	rs62278540
Chromosome Location	chr3:98622467-98622468
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	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207331	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs62276868	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62276943	1.00[AFR][1000 genomes]
rs62278489	1.00[AFR][1000 genomes]
rs62278526	1.00[AFR][1000 genomes]
rs62278535	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs62278538	1.00[AFR][1000 genomes]
rs7617405	0.90[EUR][1000 genomes]
rs7623952	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98621200-98622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:98621400-98622600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:98621400-98625000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:98621600-98625000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:98621600-98625200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:98621600-98625400	Weak transcription	Psoas Muscle	Psoas
7	chr3:98621800-98623000	Weak transcription	HUVEC	blood vessel
8	chr3:98621800-98623000	Enhancers	NHDF-Ad	bronchial
9	chr3:98621800-98623200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:98621800-98625000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:98621800-98625000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:98621800-98625000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:98621800-98625000	Weak transcription	Fetal Brain Male	brain
14	chr3:98621800-98625000	Weak transcription	Hela-S3	cervix
15	chr3:98621800-98625000	Weak transcription	HSMMtube	muscle
16	chr3:98622000-98624000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:98622000-98624000	Enhancers	NH-A	brain
18	chr3:98622000-98625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:98622000-98625000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:98622000-98625200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:98622200-98622800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:98622200-98622800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:98622200-98622800	Weak transcription	NHLF	lung
24	chr3:98622200-98623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:98622200-98623200	Weak transcription	Fetal Heart	heart
26	chr3:98622200-98623600	Enhancers	NHEK	skin
27	chr3:98622200-98624000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:98622200-98625000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98622200-98625000	Weak transcription	Fetal Lung	lung
30	chr3:98622200-98625000	Weak transcription	HMEC	breast
31	chr3:98622200-98625000	Weak transcription	HSMM	muscle
32	chr3:98622200-98625200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:98622400-98622600	Enhancers	A549	lung
34	chr3:98622400-98622800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:98622400-98622800	Weak transcription	Osteobl	bone

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