Variant report

Variant	rs71439299
Chromosome Location	chr2:40678014-40678015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12996425	0.89[EUR][1000 genomes]
rs12999886	0.84[EUR][1000 genomes]
rs13025964	0.82[ASN][1000 genomes]
rs13031545	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13031785	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13031843	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13031849	0.87[EUR][1000 genomes]
rs13035085	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17025999	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17026001	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17026003	0.87[EUR][1000 genomes]
rs17026005	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17026009	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17026011	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17026012	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17026014	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17026018	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34038561	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34205507	0.82[ASN][1000 genomes]
rs34214503	0.81[ASN][1000 genomes]
rs34272753	0.81[ASN][1000 genomes]
rs34682370	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35306270	0.82[ASN][1000 genomes]
rs35321042	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35478019	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35797248	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35920920	0.87[EUR][1000 genomes]
rs35923316	0.84[EUR][1000 genomes]
rs4140728	0.80[ASN][1000 genomes]
rs57193459	0.87[EUR][1000 genomes]
rs61629255	0.81[EUR][1000 genomes]
rs6736874	0.81[ASN][1000 genomes]
rs71439297	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71439298	0.83[AMR][1000 genomes];0.89[EUR][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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv2700	chr2:40667461-40712805	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40672200-40678200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:40674000-40679600	Enhancers	Fetal Heart	heart
3	chr2:40675200-40680000	Active TSS	Brain Anterior Caudate	brain
4	chr2:40675600-40680000	Active TSS	Fetal Brain Female	brain
5	chr2:40676400-40679600	Active TSS	Stomach Smooth Muscle	stomach
6	chr2:40676400-40680200	Active TSS	NHLF	lung
7	chr2:40676600-40680000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:40676800-40678200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:40676800-40679600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:40676800-40680000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:40676800-40680200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:40677000-40678600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:40677000-40679400	Active TSS	Fetal Intestine Small	intestine
14	chr2:40677000-40679800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr2:40677000-40679800	Active TSS	Aorta	Aorta
16	chr2:40677000-40679800	Active TSS	Brain Germinal Matrix	brain
17	chr2:40677000-40679800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr2:40677000-40680000	Active TSS	Brain Cingulate Gyrus	brain
19	chr2:40677000-40680000	Active TSS	Fetal Kidney	kidney
20	chr2:40677000-40680000	Active TSS	Fetal Stomach	stomach
21	chr2:40677000-40680000	Active TSS	NH-A	brain
22	chr2:40677000-40680000	Active TSS	NHDF-Ad	bronchial
23	chr2:40677000-40680200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr2:40677200-40678200	Active TSS	Fetal Muscle Trunk	muscle
25	chr2:40677200-40678400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
26	chr2:40677200-40678400	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr2:40677200-40678400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
28	chr2:40677200-40678600	Active TSS	Right Ventricle	heart
29	chr2:40677200-40678800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr2:40677200-40679000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:40677200-40679200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
32	chr2:40677200-40679600	Active TSS	Thymus	Thymus
33	chr2:40677200-40679800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:40677200-40679800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:40677200-40679800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:40677200-40679800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:40677200-40679800	Active TSS	Ovary	ovary
38	chr2:40677200-40679800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr2:40677200-40679800	Active TSS	Rectal Smooth Muscle	rectum
40	chr2:40677400-40678200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:40677400-40678200	Active TSS	Primary T cells from cord blood	blood
42	chr2:40677400-40678200	Active TSS	Colonic Mucosa	Colon
43	chr2:40677400-40678400	Active TSS	Duodenum Mucosa	Duodenum
44	chr2:40677400-40678400	Active TSS	Left Ventricle	heart
45	chr2:40677400-40678800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:40677400-40679600	Active TSS	Dnd41	blood
47	chr2:40677400-40679600	Active TSS	HMEC	breast
48	chr2:40677400-40679800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr2:40677400-40679800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:40677400-40679800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood

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