Variant report

Variant	rs2072530
Chromosome Location	chr2:40391516-40391517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40390508..40393940-chr2:40401107..40404487,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1012311	0.81[CEU][hapmap]
rs105287	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs106706	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12993486	0.85[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13017329	0.82[YRI][hapmap];0.93[AMR][1000 genomes]
rs1428571	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs1651354	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17025367	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17025372	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17025380	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17025588	0.85[CHD][hapmap]
rs2072529	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2270327	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2540904	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs368577	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs371492	0.90[JPT][hapmap]
rs372072	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs375311	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs376303	0.81[JPT][hapmap]
rs376535	0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs379804	0.88[ASN][1000 genomes]
rs380590	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs381610	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs385341	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]
rs385665	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs388467	0.87[ASN][1000 genomes]
rs390145	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs392317	0.81[CEU][hapmap]
rs395987	0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs398006	0.80[ASN][1000 genomes]
rs398898	0.88[ASN][1000 genomes]
rs402777	0.90[ASN][1000 genomes]
rs404005	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs404214	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs405804	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs407148	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs408263	0.81[CEU][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs409522	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs410912	0.88[ASN][1000 genomes]
rs433572	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs446538	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs447136	0.91[CHD][hapmap];0.81[JPT][hapmap]
rs449383	0.81[JPT][hapmap]
rs450450	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs473400	0.81[ASN][1000 genomes]
rs671010	0.81[ASN][1000 genomes]
rs72792740	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40358000-40392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:40358200-40392200	Weak transcription	NHLF	lung
4	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
6	chr2:40366800-40391800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:40369600-40391600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:40371800-40391800	Weak transcription	NHDF-Ad	bronchial
9	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
10	chr2:40376800-40394200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:40378200-40392000	Weak transcription	Gastric	stomach
13	chr2:40379200-40393400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:40381200-40391800	Weak transcription	Adipose Nuclei	Adipose
15	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
16	chr2:40381800-40395200	Weak transcription	Spleen	Spleen
17	chr2:40382400-40392800	Strong transcription	Dnd41	blood
18	chr2:40382600-40391800	Strong transcription	Left Ventricle	heart
19	chr2:40383000-40392400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:40383400-40392200	Weak transcription	Aorta	Aorta
21	chr2:40383400-40392600	Strong transcription	HSMM	muscle
22	chr2:40384200-40392200	Weak transcription	Fetal Kidney	kidney
23	chr2:40384600-40391800	Weak transcription	Right Ventricle	heart
24	chr2:40386000-40391600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:40386000-40395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:40386000-40395200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:40386400-40392200	Weak transcription	Fetal Brain Male	brain
28	chr2:40386400-40392200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:40386400-40395200	Weak transcription	Fetal Intestine Large	intestine
30	chr2:40387200-40392800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr2:40387800-40391600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:40387800-40391800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:40388400-40396400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:40388600-40395200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:40389000-40391800	Weak transcription	Fetal Lung	lung
36	chr2:40389000-40391800	Weak transcription	Fetal Stomach	stomach
37	chr2:40389000-40391800	Weak transcription	Ovary	ovary
38	chr2:40389200-40392000	Strong transcription	Fetal Brain Female	brain
39	chr2:40389200-40392000	Strong transcription	Osteobl	bone
40	chr2:40389400-40396200	Weak transcription	Placenta	Placenta
41	chr2:40389600-40392200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:40389600-40393000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:40390200-40391800	Weak transcription	Small Intestine	intestine
44	chr2:40390400-40391800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:40390600-40392000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:40390600-40395200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:40390800-40392000	Weak transcription	Right Atrium	heart
48	chr2:40390800-40395200	Weak transcription	Fetal Intestine Small	intestine
49	chr2:40391200-40391800	Enhancers	Fetal Thymus	thymus
50	chr2:40391200-40391800	Genic enhancers	Stomach Smooth Muscle	stomach

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