Variant report

Variant	rs6544317
Chromosome Location	chr2:40509990-40509991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11904139	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990608	0.85[ASN][1000 genomes]
rs2110744	0.84[ASN][1000 genomes]
rs2160237	0.85[ASN][1000 genomes]
rs4952402	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544318	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6748881	0.83[ASN][1000 genomes]
rs998260	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	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
4	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40500200-40514600	Weak transcription	Fetal Brain Male	brain
2	chr2:40503600-40510200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:40503600-40514800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40504000-40510600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:40504000-40510800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40506200-40510800	Enhancers	HMEC	breast
7	chr2:40506400-40510600	Enhancers	Fetal Heart	heart
8	chr2:40506400-40516800	Weak transcription	Small Intestine	intestine
9	chr2:40506600-40511000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:40506600-40514600	Weak transcription	Brain Germinal Matrix	brain
11	chr2:40506800-40510000	Weak transcription	Brain Angular Gyrus	brain
12	chr2:40506800-40510400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:40506800-40517200	Weak transcription	Dnd41	blood
14	chr2:40507400-40511000	Enhancers	NHEK	skin
15	chr2:40507600-40510600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:40507600-40511200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:40508000-40510200	Enhancers	NH-A	brain
18	chr2:40508000-40511400	Flanking Active TSS	HSMMtube	muscle
19	chr2:40508000-40517200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:40508400-40511000	Enhancers	Brain Hippocampus Middle	brain
21	chr2:40508600-40510200	Flanking Active TSS	HSMM	muscle
22	chr2:40508600-40510600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:40508600-40511400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr2:40508800-40510000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:40508800-40510400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:40508800-40510600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:40508800-40510600	Weak transcription	Right Ventricle	heart
28	chr2:40509000-40514800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:40509000-40519400	Weak transcription	Fetal Stomach	stomach
30	chr2:40509200-40510200	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:40509200-40512600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:40509200-40517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:40509400-40510000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr2:40509400-40510000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:40509400-40510000	Active TSS	Duodenum Mucosa	Duodenum
36	chr2:40509400-40510000	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr2:40509400-40510000	Active TSS	GM12878-XiMat	blood
38	chr2:40509400-40510000	Flanking Active TSS	Osteobl	bone
39	chr2:40509400-40510200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr2:40509400-40510200	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr2:40509400-40510200	Active TSS	Right Atrium	heart
42	chr2:40509400-40510200	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:40509400-40510800	Active TSS	Stomach Smooth Muscle	stomach
44	chr2:40509400-40511000	Active TSS	Aorta	Aorta
45	chr2:40509400-40511200	Active TSS	Ovary	ovary
46	chr2:40509600-40510000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:40509600-40510000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:40509600-40510000	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr2:40509600-40510000	Active TSS	Colon Smooth Muscle	Colon
50	chr2:40509600-40510000	Active TSS	Fetal Lung	lung

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