Variant report

Variant	rs379859
Chromosome Location	chr2:40468275-40468276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1641452	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1651356	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34971853	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36162999	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36184451	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs371909	0.98[ASN][1000 genomes]
rs374159	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs376491	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs378702	0.83[AMR][1000 genomes]
rs380082	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs383073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs384994	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs389992	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs391984	0.91[ASN][1000 genomes]
rs394112	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs398175	0.81[ASN][1000 genomes]
rs399061	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs401815	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs402307	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs405884	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs406736	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs407267	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs407388	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs415695	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs417464	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs427632	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs428738	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429227	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs430394	0.87[ASN][1000 genomes]
rs430473	0.80[AMR][1000 genomes]
rs432142	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs432769	0.91[ASN][1000 genomes]
rs432981	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436010	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs440155	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs442476	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442586	0.98[ASN][1000 genomes]
rs443236	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs444504	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs450823	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs451158	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs451811	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs452138	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs479909	0.87[ASN][1000 genomes]
rs4952596	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505473	0.83[ASN][1000 genomes]
rs588179	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs615449	0.98[ASN][1000 genomes]
rs666362	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674128	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs678107	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72794789	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40453800-40471000	Weak transcription	Right Ventricle	heart
4	chr2:40453800-40471400	Weak transcription	Right Atrium	heart
5	chr2:40465800-40468800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:40465800-40469600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:40466200-40468600	Enhancers	Fetal Heart	heart
8	chr2:40466600-40468600	Enhancers	NHDF-Ad	bronchial
9	chr2:40467600-40469200	Weak transcription	Psoas Muscle	Psoas
10	chr2:40467600-40469400	Weak transcription	Brain Germinal Matrix	brain
11	chr2:40467600-40471000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:40467800-40487400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:40468000-40469400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:40468000-40469400	Weak transcription	HSMMtube	muscle
15	chr2:40468000-40469600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:40468000-40469800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:40468000-40470200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:40468000-40470200	Weak transcription	NH-A	brain
19	chr2:40468000-40470400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:40468000-40470400	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:40468000-40470400	Weak transcription	HSMM	muscle
22	chr2:40468000-40470400	Weak transcription	NHLF	lung
23	chr2:40468000-40470600	Weak transcription	Fetal Stomach	stomach
24	chr2:40468000-40470800	Weak transcription	Left Ventricle	heart
25	chr2:40468000-40470800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:40468000-40471000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:40468000-40471200	Weak transcription	Colonic Mucosa	Colon
28	chr2:40468000-40472000	Weak transcription	Fetal Lung	lung
29	chr2:40468000-40476600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:40468200-40469600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:40468200-40469800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:40468200-40470000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:40468200-40470200	Weak transcription	Osteobl	bone
34	chr2:40468200-40470400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:40468200-40470600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:40468200-40471000	Weak transcription	Adipose Nuclei	Adipose

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