Variant report

Variant	rs28682325
Chromosome Location	chr2:54700447-54700448
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	chr2:54698509..54700460-chr2:54784442..54786453,2	MCF-7	breast:
2	chr2:54699717..54702089-chr2:54703143..54705442,2	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10153583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10153704	0.89[EUR][1000 genomes]
rs12328732	0.96[EUR][1000 genomes]
rs13391816	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13391936	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13403941	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409277	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17045932	0.89[EUR][1000 genomes]
rs28380233	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28441070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28698551	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3693290	chr2:54693204-54707562	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv438348	chr2:54693204-54714066	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv817939	chr2:54693204-54718181	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54687000-54700800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:54695200-54701800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:54695600-54701200	Enhancers	Brain Angular Gyrus	brain
4	chr2:54695600-54701400	Enhancers	Adipose Nuclei	Adipose
5	chr2:54695600-54701400	Enhancers	Brain Substantia Nigra	brain
6	chr2:54695600-54701800	Enhancers	Brain Anterior Caudate	brain
7	chr2:54695600-54701800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:54695800-54701600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:54696200-54701200	Enhancers	Fetal Brain Male	brain
10	chr2:54696200-54701800	Enhancers	Brain Hippocampus Middle	brain
11	chr2:54696800-54703600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:54697200-54700600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:54697200-54701200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54697200-54707200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:54697200-54709600	Weak transcription	Placenta	Placenta
16	chr2:54697400-54700600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:54698400-54701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:54698600-54701400	Enhancers	HSMM	muscle
19	chr2:54698800-54700600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:54698800-54700600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:54698800-54701000	Weak transcription	Ovary	ovary
22	chr2:54698800-54701400	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:54698800-54701600	Enhancers	Fetal Lung	lung
24	chr2:54698800-54702600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:54698800-54702600	Weak transcription	Gastric	stomach
26	chr2:54698800-54702600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:54698800-54702600	Weak transcription	Spleen	Spleen
28	chr2:54698800-54703400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:54698800-54705200	Weak transcription	Lung	lung
30	chr2:54698800-54707200	Weak transcription	Pancreas	Pancrea
31	chr2:54699000-54701000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:54699000-54701000	Enhancers	Fetal Heart	heart
33	chr2:54699000-54701000	Weak transcription	Fetal Stomach	stomach
34	chr2:54699000-54702400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:54699000-54702600	Weak transcription	Right Atrium	heart
36	chr2:54699000-54706000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:54699200-54706200	Weak transcription	HUVEC	blood vessel
38	chr2:54699600-54700600	Enhancers	HSMMtube	muscle
39	chr2:54699600-54701000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:54699600-54701800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr2:54699600-54703200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:54699600-54706600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:54699600-54709200	Weak transcription	Aorta	Aorta
44	chr2:54699800-54701000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:54699800-54701000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:54699800-54702400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:54699800-54702400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:54699800-54703200	Weak transcription	Fetal Brain Female	brain
49	chr2:54699800-54707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:54699800-54709600	Weak transcription	Osteobl	bone

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