Variant report

Variant	rs820546
Chromosome Location	chr3:112405506-112405507
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112401424..112402927-chr3:112404953..112407128,2	K562	blood:
2	chr3:112396444..112398004-chr3:112404966..112407512,2	MCF-7	breast:
3	chr3:112404774..112406645-chr3:112438541..112440908,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1154270	1.00[MEX][hapmap]
rs1154271	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1387022	1.00[MEX][hapmap]
rs7642576	1.00[MEX][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs820546	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112391400-112407800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112397000-112406000	Weak transcription	K562	blood
3	chr3:112400400-112408200	Enhancers	NHLF	lung
4	chr3:112400600-112406600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:112400600-112408800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:112401000-112408800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:112401200-112406000	Enhancers	A549	lung
8	chr3:112401200-112413800	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:112401400-112408200	Enhancers	Osteobl	bone
10	chr3:112401600-112407000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:112401800-112407600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:112402600-112407800	Enhancers	NHDF-Ad	bronchial
13	chr3:112403000-112407400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:112403200-112407000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:112403200-112409200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:112403400-112406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:112403400-112407000	Weak transcription	HMEC	breast
18	chr3:112403400-112407000	Weak transcription	NHEK	skin
19	chr3:112403400-112409200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:112403600-112409600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:112404000-112409400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:112404200-112408600	Weak transcription	Primary T cells from cord blood	blood
23	chr3:112404200-112408800	Enhancers	NH-A	brain
24	chr3:112404400-112406000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:112404400-112406400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:112404400-112406800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:112404400-112408200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:112404400-112408800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:112404600-112406000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:112404600-112406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:112405000-112406000	Weak transcription	HSMM	muscle
32	chr3:112405000-112406400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:112405000-112406400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:112405200-112405600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:112405200-112405800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:112405200-112406400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:112405200-112406600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:112405200-112409000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:112405200-112409200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:112405400-112405800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:112405400-112405800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:112405400-112406600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:112405400-112411800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:112405400-112412000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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