Variant report

Variant	rs385341
Chromosome Location	chr2:40400489-40400490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs105287	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs106706	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12993486	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13017329	0.82[AMR][1000 genomes]
rs1428571	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1651354	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17025367	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17025372	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17025380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17025588	0.89[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2072529	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2072530	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2270327	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2540904	0.89[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs368577	0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs368613	0.85[ASN][1000 genomes]
rs371492	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs372072	0.93[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs373273	0.82[ASN][1000 genomes]
rs376303	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs376535	0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs379804	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs380590	0.81[CHD][hapmap]
rs381610	0.86[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs385665	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs388467	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs390145	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs392953	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs395755	0.83[ASN][1000 genomes]
rs395987	0.89[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs398006	0.86[ASN][1000 genomes]
rs398898	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs402777	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs404005	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs404214	0.89[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs404226	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs405804	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs407148	0.89[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs408263	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs409522	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410912	0.93[ASN][1000 genomes]
rs419125	0.81[ASN][1000 genomes]
rs433572	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs435404	0.82[JPT][hapmap]
rs446538	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs447136	0.89[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs449383	0.80[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs450450	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs473400	0.84[ASN][1000 genomes]
rs481800	0.81[ASN][1000 genomes]
rs530048	0.81[ASN][1000 genomes]
rs62148799	0.81[ASN][1000 genomes]
rs671010	0.84[ASN][1000 genomes]
rs72792740	0.83[AMR][1000 genomes];0.88[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:30 , 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	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
5	chr2:40392600-40405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
7	chr2:40393200-40401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
9	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:40396400-40405400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:40396600-40401800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:40397000-40405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:40397600-40401600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:40397600-40404800	Weak transcription	Right Ventricle	heart
15	chr2:40397800-40404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:40398200-40404800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:40398400-40406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:40399200-40404800	Weak transcription	Left Ventricle	heart
19	chr2:40399400-40404800	Weak transcription	Dnd41	blood
20	chr2:40399600-40400600	Weak transcription	HSMM	muscle
21	chr2:40399600-40402200	Weak transcription	Fetal Heart	heart
22	chr2:40400000-40400800	Enhancers	NHDF-Ad	bronchial
23	chr2:40400000-40404600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:40400200-40400600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:40400200-40400600	Enhancers	Osteobl	bone
26	chr2:40400200-40400800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:40400200-40401000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:40400400-40400800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:40400400-40401000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:40400400-40401000	Enhancers	Muscle Satellite Cultured Cells	--

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