Variant report

Variant	rs56405280
Chromosome Location	chr2:234291755-234291756
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	chr2:234179050..234180809-chr2:234289947..234292928,2	MCF-7	breast:
2	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1046976	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675531	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11679008	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13384918	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13420688	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55684040	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55693723	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55804614	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55893802	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56082182	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58280122	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72978363	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72978374	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72978375	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72980318	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7573866	0.95[EUR][1000 genomes]
rs7598771	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:234264800-234292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:234265000-234295000	Weak transcription	Osteobl	bone
4	chr2:234265200-234295000	Weak transcription	NH-A	brain
5	chr2:234265800-234293000	Weak transcription	HMEC	breast
6	chr2:234266000-234292400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:234266000-234292600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:234266000-234293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:234266400-234294000	Weak transcription	Fetal Brain Male	brain
10	chr2:234268400-234293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:234269200-234293400	Weak transcription	Right Atrium	heart
12	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:234273000-234292200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:234277200-234292600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:234278600-234292200	Weak transcription	Ovary	ovary
19	chr2:234278600-234292800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:234278600-234292800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:234278600-234293000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:234278600-234293600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:234278600-234293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:234278600-234294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:234278600-234294000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:234278800-234293000	Weak transcription	Brain Substantia Nigra	brain
27	chr2:234279000-234292600	Weak transcription	NHEK	skin
28	chr2:234279000-234293000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:234279200-234293200	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:234279200-234293400	Weak transcription	Brain Anterior Caudate	brain
31	chr2:234279200-234293600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:234279200-234294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:234280600-234293200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:234282000-234292000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:234282000-234292800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:234282200-234293000	Weak transcription	Gastric	stomach
39	chr2:234282200-234293400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:234282200-234293600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:234282400-234294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:234282400-234298000	Weak transcription	Dnd41	blood
43	chr2:234284000-234293800	Weak transcription	Colonic Mucosa	Colon
44	chr2:234284600-234292800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:234284800-234292400	Weak transcription	Fetal Lung	lung
46	chr2:234284800-234292800	Weak transcription	HSMM	muscle
47	chr2:234284800-234295400	Weak transcription	Fetal Intestine Large	intestine
48	chr2:234285000-234295400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:234285800-234292200	Weak transcription	Primary T cells from cord blood	blood
50	chr2:234286400-234291800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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