Variant report

Variant	rs4339084
Chromosome Location	chr3:113552457-113552458
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	chr3:113546118..113548286-chr3:113550163..113552651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178075	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11706726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631130	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163388	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399490	0.82[ASN][1000 genomes]
rs2399491	0.82[ASN][1000 genomes]
rs2712334	0.81[ASN][1000 genomes]
rs2712366	0.83[ASN][1000 genomes]
rs4682502	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62265385	0.82[ASN][1000 genomes]
rs736360	0.81[ASN][1000 genomes]
rs7628746	0.81[ASN][1000 genomes]
rs7636168	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7646203	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv482804	chr3:113432431-113581672	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv432478	chr3:113492402-113614489	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv460822	chr3:113543081-113600970	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv591302	chr3:113543081-113600970	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4339084	GRAMD1C	cis	Adipose Subcutaneous	GTEx
rs4339084	GRAMD1C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113548600-113552600	Enhancers	HepG2	liver
2	chr3:113549400-113557600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:113549600-113557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:113549800-113557600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:113549800-113557600	Weak transcription	NHDF-Ad	bronchial
6	chr3:113550000-113553000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:113550000-113554200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:113550000-113554200	Weak transcription	Stomach Mucosa	stomach
9	chr3:113550000-113557200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:113550000-113557400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:113550000-113557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:113550000-113557600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:113550200-113553800	Weak transcription	NHEK	skin
14	chr3:113550600-113553800	Weak transcription	Hela-S3	cervix
15	chr3:113550800-113552600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:113551000-113552600	Enhancers	Primary T cells from cord blood	blood
17	chr3:113551200-113554000	Weak transcription	HUVEC	blood vessel
18	chr3:113551400-113552600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:113551600-113552600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:113551800-113552600	Enhancers	GM12878-XiMat	blood
21	chr3:113551800-113554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:113551800-113554200	Weak transcription	HMEC	breast
23	chr3:113551800-113557400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:113552000-113554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:113552200-113557000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:113552400-113552800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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