Variant report

Variant	rs59093347
Chromosome Location	chr2:54270503-54270504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54263866..54266283-chr2:54268179..54270997,2	MCF-7	breast:
2	chr2:54214676..54216240-chr2:54269746..54271307,2	MCF-7	breast:
3	chr2:54196754..54199242-chr2:54269928..54271642,2	K562	blood:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12052354	0.87[ASN][1000 genomes]
rs12613999	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12619131	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13426329	0.96[ASN][1000 genomes]
rs1559038	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57220223	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57925923	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58015041	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60702118	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61231824	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54246800-54275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:54248600-54278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
4	chr2:54248800-54275600	Weak transcription	Primary B cells from cord blood	blood
5	chr2:54258000-54272200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:54260000-54272200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:54260400-54278200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:54265200-54272400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:54265200-54272600	Enhancers	HMEC	breast
10	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
11	chr2:54266400-54271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:54266400-54271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:54266800-54272200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:54267000-54272600	Weak transcription	Fetal Stomach	stomach
15	chr2:54267400-54272000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:54267800-54271800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:54268000-54271400	Enhancers	Osteobl	bone
18	chr2:54268200-54270800	Strong transcription	Primary T cells from cord blood	blood
19	chr2:54268200-54275000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
21	chr2:54268400-54270800	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:54268600-54270800	Weak transcription	NHEK	skin
25	chr2:54268600-54272400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:54268600-54275400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:54268800-54275000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:54268800-54275400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:54268800-54278200	Weak transcription	Pancreas	Pancrea
30	chr2:54269000-54270800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:54269400-54271000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:54269600-54271200	Enhancers	Brain Substantia Nigra	brain
33	chr2:54269600-54272000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:54269600-54272200	Enhancers	Brain Angular Gyrus	brain
35	chr2:54269800-54270600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:54269800-54270600	Enhancers	Fetal Muscle Leg	muscle
37	chr2:54269800-54271200	Enhancers	Fetal Heart	heart
38	chr2:54269800-54271600	Enhancers	A549	lung
39	chr2:54269800-54271800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:54270000-54270600	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:54270000-54271000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:54270000-54271000	Enhancers	HepG2	liver
43	chr2:54270000-54271800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:54270000-54271800	Enhancers	Psoas Muscle	Psoas
45	chr2:54270000-54274000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54270200-54271000	Weak transcription	Aorta	Aorta
47	chr2:54270200-54272000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:54270200-54272000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:54270200-54272400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:54270200-54276600	Weak transcription	Colon Smooth Muscle	Colon

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