Variant report

Variant	rs2780276
Chromosome Location	chr1:112962548-112962549
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	chr1:112961598..112963663-chr1:113006569..113008667,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1175624	1.00[AFR][1000 genomes]
rs1175627	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1175628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175637	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175639	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1175640	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175642	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175643	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175644	0.87[AFR][1000 genomes]
rs1759691	0.87[AFR][1000 genomes]
rs1777621	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2483347	0.96[AFR][1000 genomes]
rs2780274	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2798246	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1850997	chr1:112944472-112993754	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112942400-112988200	Weak transcription	Small Intestine	intestine
2	chr1:112942600-112966400	Weak transcription	Spleen	Spleen
3	chr1:112942600-112967000	Weak transcription	Pancreas	Pancrea
4	chr1:112945000-112966400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:112946800-112970600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:112947200-112971200	Weak transcription	Aorta	Aorta
7	chr1:112947200-112981000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:112947400-112965600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:112949200-112963200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:112949200-112966400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:112951200-112969000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:112951600-112968800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:112952000-112969600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:112952400-112990600	Weak transcription	Esophagus	oesophagus
15	chr1:112952600-112963400	Weak transcription	Stomach Mucosa	stomach
16	chr1:112952600-112981400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:112953800-112966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:112954400-112962600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:112954400-112962600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:112954400-112962600	Strong transcription	HUVEC	blood vessel
21	chr1:112954400-112963200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:112954400-112963400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:112954400-112963800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:112954400-112964000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:112954400-112964600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:112954400-112967400	Strong transcription	Osteobl	bone
27	chr1:112954600-112962800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:112954800-112962600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:112956200-112963200	Weak transcription	NHEK	skin
30	chr1:112957400-112986600	Weak transcription	NHLF	lung
31	chr1:112957600-112967400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:112957600-112997600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:112958000-112964600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr1:112958200-112967600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:112958600-112962800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:112958600-112971000	Weak transcription	Right Ventricle	heart
37	chr1:112958600-112979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:112959000-112965800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:112959400-112962800	Weak transcription	Fetal Intestine Small	intestine
40	chr1:112959600-112965400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:112959600-112973200	Weak transcription	Lung	lung
42	chr1:112959600-112991600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:112959800-112972000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:112959800-112973400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:112959800-112992800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:112960000-112962800	Weak transcription	Fetal Stomach	stomach
47	chr1:112960000-112965200	Weak transcription	NHDF-Ad	bronchial
48	chr1:112960000-112967600	Weak transcription	Colonic Mucosa	Colon
49	chr1:112960000-112968200	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:112960000-112972200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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