Variant report

Variant	rs406880
Chromosome Location	chr2:40398512-40398513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs105288	1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs118899	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641456	0.89[ASN][1000 genomes]
rs1641457	0.89[ASN][1000 genomes]
rs1641458	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1651355	0.89[ASN][1000 genomes]
rs28628343	0.97[ASN][1000 genomes]
rs35487690	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs366578	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs368642	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs369140	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs371909	1.00[JPT][hapmap]
rs372052	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs373602	0.95[ASN][1000 genomes]
rs373606	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs374711	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3749056	1.00[JPT][hapmap]
rs375180	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs376170	0.89[ASN][1000 genomes]
rs376491	0.84[ASN][1000 genomes]
rs379410	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs380082	1.00[JPT][hapmap]
rs380975	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs384511	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs384791	0.89[ASN][1000 genomes]
rs384994	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs385561	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs389109	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs389992	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs391631	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs391984	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs393711	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs394112	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs394540	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs395404	0.86[JPT][hapmap]
rs399061	1.00[JPT][hapmap]
rs401815	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs402307	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs405884	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs406222	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs407267	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs407388	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs408009	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs408662	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs410031	0.86[ASN][1000 genomes]
rs410480	0.88[ASN][1000 genomes]
rs413711	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs414766	0.86[ASN][1000 genomes]
rs415695	1.00[JPT][hapmap]
rs417464	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs417591	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs417873	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs418380	0.89[ASN][1000 genomes]
rs418780	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421870	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422411	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs423075	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs426295	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs427632	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs428738	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs430314	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs430473	0.87[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs434082	1.00[JPT][hapmap]
rs434326	0.89[ASN][1000 genomes]
rs436010	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs439960	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs440155	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs441196	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs441413	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441593	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs441802	0.87[ASN][1000 genomes]
rs442586	1.00[JPT][hapmap]
rs443236	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs450116	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs450823	1.00[JPT][hapmap]
rs451074	0.86[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451158	1.00[JPT][hapmap]
rs451811	1.00[JPT][hapmap]
rs452138	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs505473	1.00[JPT][hapmap]
rs581477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs581568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615449	1.00[JPT][hapmap]
rs666362	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs678107	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs679339	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs688673	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
3	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
4	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
7	chr2:40392600-40405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
9	chr2:40393200-40401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:40393400-40400000	Weak transcription	NHDF-Ad	bronchial
11	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
12	chr2:40393800-40399000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:40395400-40400400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:40396400-40400000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:40396400-40400200	Weak transcription	Osteobl	bone
17	chr2:40396400-40405400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:40396600-40400200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:40396600-40401800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:40396800-40400400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:40397000-40399200	Strong transcription	Left Ventricle	heart
22	chr2:40397000-40405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:40397200-40399600	Strong transcription	HSMM	muscle
24	chr2:40397200-40400200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40397400-40399400	Strong transcription	Dnd41	blood
26	chr2:40397400-40399600	Genic enhancers	Fetal Heart	heart
27	chr2:40397600-40401600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:40397600-40404800	Weak transcription	Right Ventricle	heart
29	chr2:40397800-40404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:40398200-40404800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:40398400-40406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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