Variant report

Variant	rs820559
Chromosome Location	chr3:112466376-112466377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112278451..112281169-chr3:112466155..112467753,2	K562	blood:
2	chr3:112465788..112467955-chr3:112468785..112471247,2	K562	blood:
3	chr13:50509795..50512385-chr3:112464979..112467287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123178	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs59168637	0.87[ASN][1000 genomes]
rs820542	0.84[EUR][1000 genomes]
rs820553	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820563	0.86[EUR][1000 genomes]
rs820567	0.85[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112458400-112467800	Weak transcription	Stomach Mucosa	stomach
2	chr3:112458800-112467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:112459000-112467000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:112459000-112470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:112459200-112466400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:112459200-112467800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:112461400-112466400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:112461400-112466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:112462600-112468000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:112464200-112468000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:112464200-112469200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:112464400-112469200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:112464400-112470800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:112465000-112467000	Weak transcription	GM12878-XiMat	blood
15	chr3:112465000-112469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:112465000-112469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:112465400-112468200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr3:112465600-112467400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr3:112465800-112466600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:112465800-112467800	Weak transcription	HMEC	breast
21	chr3:112465800-112468000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:112465800-112470800	Weak transcription	NHDF-Ad	bronchial
23	chr3:112466000-112467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:112466000-112467200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:112466000-112467600	Enhancers	A549	lung
26	chr3:112466000-112468000	Enhancers	K562	blood
27	chr3:112466000-112469200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:112466200-112470400	Weak transcription	NH-A	brain
29	chr3:112466200-112470400	Weak transcription	Osteobl	bone

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