Variant report

Variant	rs13031843
Chromosome Location	chr2:40664721-40664722
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	chr2:40663877..40665800-chr2:40669222..40671159,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10490043	0.82[CEU][hapmap]
rs12052800	0.81[TSI][hapmap]
rs12988659	0.90[TSI][hapmap]
rs12996425	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap]
rs12999886	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13017237	0.90[TSI][hapmap]
rs13031545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13035085	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17025926	0.82[CEU][hapmap]
rs17025999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026003	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990609	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs34038561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34682370	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35321042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35478019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35797248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35923316	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4993292	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[ASN][1000 genomes]
rs57193459	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61629255	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71439297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71439298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71439299	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7603114	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs9789739	0.90[TSI][hapmap]

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	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
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
4	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:40655000-40665000	Weak transcription	Fetal Brain Male	brain
6	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
7	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
8	chr2:40658200-40665400	Enhancers	NHLF	lung
9	chr2:40659800-40665600	Weak transcription	Dnd41	blood
10	chr2:40661800-40666000	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:40662200-40665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:40662400-40665000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:40662400-40665200	Enhancers	Stomach Smooth Muscle	stomach
14	chr2:40662600-40667800	Weak transcription	Primary B cells from cord blood	blood
15	chr2:40662600-40677200	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:40663000-40665200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:40663400-40666000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:40663400-40666200	Weak transcription	Hela-S3	cervix
19	chr2:40663400-40666600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:40663400-40672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:40663600-40665000	Weak transcription	Osteobl	bone
22	chr2:40663600-40665200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:40663600-40677000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:40663600-40677000	Weak transcription	Aorta	Aorta
25	chr2:40663800-40664800	Enhancers	Brain Anterior Caudate	brain
26	chr2:40663800-40665000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:40663800-40665000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:40663800-40665200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:40663800-40665200	Weak transcription	HSMM	muscle
30	chr2:40663800-40665800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:40663800-40666200	Weak transcription	NHEK	skin
32	chr2:40663800-40666800	Weak transcription	NH-A	brain
33	chr2:40663800-40667800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:40663800-40677600	Weak transcription	HSMMtube	muscle
35	chr2:40664000-40667000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:40664200-40666000	Weak transcription	HMEC	breast
37	chr2:40664200-40667400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:40664200-40667800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:40664400-40665200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:40664400-40667200	Enhancers	NHDF-Ad	bronchial
41	chr2:40664600-40665200	Weak transcription	Right Atrium	heart
42	chr2:40664600-40665400	Flanking Active TSS	Fetal Heart	heart
43	chr2:40664600-40666200	Weak transcription	Right Ventricle	heart
44	chr2:40664600-40667600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:40664600-40673000	Weak transcription	Left Ventricle	heart

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