Variant report

Variant	rs2688604
Chromosome Location	chr3:112414591-112414592
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	chr3:112361555..112362103-chr3:112413849..112414794,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35A5-3	chr3:112414248-112415003	NONHSAT091194

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

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

rs_ID	r²[population]
rs1094047	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1249921	1.00[AMR][1000 genomes]
rs1249923	1.00[AMR][1000 genomes]
rs1249924	1.00[AMR][1000 genomes]
rs1249926	1.00[AMR][1000 genomes]
rs1249927	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1615696	1.00[AMR][1000 genomes]
rs2971202	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4082839	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs820540	1.00[AMR][1000 genomes]
rs820574	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs820575	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs820576	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs820577	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs864239	0.88[AFR][1000 genomes];1.00[AMR][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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv979866	chr3:112409140-112416297	Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112407400-112415000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:112409400-112414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:112409400-112418200	Weak transcription	A549	lung
4	chr3:112409400-112418400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:112412200-112416200	Weak transcription	K562	blood
6	chr3:112412600-112418200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:112412800-112415200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:112413400-112415600	Enhancers	NHLF	lung
9	chr3:112413400-112415800	Enhancers	HSMM	muscle
10	chr3:112413400-112415800	Enhancers	HSMMtube	muscle
11	chr3:112413600-112414600	Enhancers	Stomach Smooth Muscle	stomach
12	chr3:112413600-112414800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:112413600-112415000	Enhancers	Ovary	ovary
14	chr3:112413800-112414600	Enhancers	Psoas Muscle	Psoas
15	chr3:112413800-112415000	Enhancers	Colon Smooth Muscle	Colon
16	chr3:112413800-112415200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:112413800-112415200	Enhancers	Osteobl	bone
18	chr3:112413800-112415600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:112413800-112416000	Enhancers	NHDF-Ad	bronchial
20	chr3:112414000-112414800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:112414200-112415200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:112414200-112417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:112414400-112414800	Enhancers	Skeletal Muscle Female	skeletal muscle

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