Variant report

Variant	rs56840594
Chromosome Location	chr2:110402025-110402026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110402025..110402675-chr2:110448094..110448680,2	MCF-7	breast:
2	chr2:110370732..110372780-chr2:110400593..110403257,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10496431	0.92[AMR][1000 genomes]
rs11265637	0.85[AMR][1000 genomes]
rs12612457	0.89[AMR][1000 genomes]
rs12619004	0.97[AMR][1000 genomes]
rs12622443	0.92[AMR][1000 genomes]
rs13385504	0.88[AMR][1000 genomes]
rs2867909	0.84[ASN][1000 genomes]
rs2867910	0.84[ASN][1000 genomes]
rs2903696	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2903697	0.82[ASN][1000 genomes]
rs3886070	0.97[AMR][1000 genomes]
rs57538421	0.89[ASN][1000 genomes]
rs58149954	0.89[ASN][1000 genomes]
rs58360057	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58602175	0.97[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58958362	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59185208	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59328146	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs60524887	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61354480	0.92[AMR][1000 genomes]
rs61398276	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61449947	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs717188	0.92[AMR][1000 genomes]
rs72826820	0.89[ASN][1000 genomes]
rs72826823	0.89[ASN][1000 genomes]
rs72936489	0.86[AMR][1000 genomes]
rs72938233	0.88[AMR][1000 genomes]
rs72938234	0.92[AMR][1000 genomes]
rs72938241	0.92[AMR][1000 genomes]
rs72938253	0.92[AMR][1000 genomes]
rs72938256	0.92[AMR][1000 genomes]
rs72938267	0.92[AMR][1000 genomes]
rs72938273	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72938290	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72940203	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72940214	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72940230	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72940234	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72949195	0.84[AMR][1000 genomes]
rs72949197	0.82[AMR][1000 genomes]
rs72949199	0.82[AMR][1000 genomes]
rs72949201	0.86[AMR][1000 genomes]
rs730988	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer 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 target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv999552	chr2:110396395-110978224	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110393800-110402200	Weak transcription	Fetal Thymus	thymus
2	chr2:110393800-110402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:110396200-110402200	Weak transcription	Lung	lung
4	chr2:110400600-110403800	Enhancers	Fetal Intestine Large	intestine
5	chr2:110400600-110406600	Enhancers	Placenta	Placenta
6	chr2:110400800-110403200	Enhancers	Fetal Intestine Small	intestine
7	chr2:110401000-110402400	Enhancers	Esophagus	oesophagus
8	chr2:110401000-110403800	Enhancers	Pancreas	Pancrea
9	chr2:110401200-110402200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:110401400-110404000	Enhancers	Fetal Muscle Trunk	muscle
11	chr2:110401600-110402800	Enhancers	GM12878-XiMat	blood
12	chr2:110401800-110402200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:110401800-110402200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:110401800-110402200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:110401800-110402200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:110401800-110402200	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:110401800-110402200	Active TSS	Colonic Mucosa	Colon
18	chr2:110401800-110402200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:110401800-110402200	Flanking Active TSS	HepG2	liver
20	chr2:110401800-110402400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:110401800-110402400	Enhancers	HMEC	breast
22	chr2:110401800-110402600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:110401800-110402600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:110401800-110402600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:110401800-110402600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr2:110401800-110402800	Flanking Active TSS	Liver	Liver
27	chr2:110401800-110402800	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:110401800-110402800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr2:110401800-110402800	Enhancers	Osteobl	bone
30	chr2:110401800-110403000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:110401800-110403000	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:110401800-110403000	Enhancers	Stomach Mucosa	stomach
33	chr2:110401800-110403200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:110401800-110403200	Enhancers	Fetal Muscle Leg	muscle
35	chr2:110401800-110403400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:110401800-110403400	Enhancers	NHEK	skin
37	chr2:110401800-110403600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:110401800-110403600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:110401800-110403600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:110401800-110403800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr2:110401800-110403800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:110401800-110403800	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:110401800-110404000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:110402000-110402200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr2:110402000-110402400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:110402000-110402400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:110402000-110402400	Active TSS	Brain Anterior Caudate	brain
48	chr2:110402000-110402600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:110402000-110402600	Enhancers	Rectal Smooth Muscle	rectum
50	chr2:110402000-110402600	Enhancers	HSMMtube	muscle

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