Variant report

Variant	rs56246233
Chromosome Location	chr3:49893245-49893246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49891965..49895757-chr3:49941315..49943532,3	MCF-7	breast:
2	chr3:49893084..49895699-chr3:49898396..49900154,2	MCF-7	breast:
3	chr3:49892284..49895111-chr3:49976165..49977880,2	K562	blood:
4	chr3:49892535..49894935-chr3:49965699..49968471,2	K562	blood:

Variant related genes	Relation type
ENSG00000164077	Chromatin interaction
ENSG00000004534	Chromatin interaction
ENSG00000164076	Chromatin interaction
ENSG00000228008	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2777892	1.00[AMR][1000 genomes]
rs57067759	1.00[AFR][1000 genomes]
rs58588000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6776029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6807837	1.00[AFR][1000 genomes]
rs939376	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49877000-49893400	Weak transcription	HSMMtube	muscle
2	chr3:49880800-49893400	Weak transcription	Left Ventricle	heart
3	chr3:49882800-49893400	Weak transcription	Pancreas	Pancrea
4	chr3:49884200-49893400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:49892600-49894800	Flanking Active TSS	Dnd41	blood
6	chr3:49893000-49893400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:49893000-49893400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:49893000-49893400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:49893000-49893400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49893000-49893400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49893000-49893400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:49893000-49893400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:49893000-49893400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:49893000-49893400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:49893000-49893400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49893000-49893400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:49893000-49893400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:49893000-49893400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:49893000-49893400	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:49893000-49893400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:49893000-49893400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:49893000-49893400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:49893000-49893400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:49893000-49893400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:49893000-49893400	Enhancers	Brain Hippocampus Middle	brain
26	chr3:49893000-49893400	Enhancers	Fetal Brain Male	brain
27	chr3:49893000-49893400	Enhancers	Fetal Heart	heart
28	chr3:49893000-49893400	Enhancers	Fetal Intestine Large	intestine
29	chr3:49893000-49893400	Enhancers	Fetal Stomach	stomach
30	chr3:49893000-49893400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr3:49893000-49893400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr3:49893000-49893400	Enhancers	Right Ventricle	heart
33	chr3:49893000-49893400	Flanking Active TSS	HepG2	liver
34	chr3:49893000-49893400	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr3:49893000-49893600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:49893000-49893600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:49893000-49893600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:49893000-49893600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:49893000-49893600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr3:49893000-49893600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:49893000-49893600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:49893000-49893600	Flanking Active TSS	Fetal Brain Female	brain
43	chr3:49893000-49893600	Enhancers	Small Intestine	intestine
44	chr3:49893000-49893600	Enhancers	Spleen	Spleen
45	chr3:49893000-49893600	Flanking Active TSS	GM12878-XiMat	blood
46	chr3:49893000-49893600	Flanking Active TSS	HMEC	breast
47	chr3:49893000-49893600	Flanking Active TSS	NH-A	brain
48	chr3:49893000-49893600	Flanking Active TSS	NHDF-Ad	bronchial
49	chr3:49893000-49893800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:49893000-49893800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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