Variant report

Variant	rs407889
Chromosome Location	chr2:40392704-40392705
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: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs105288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs118899	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641456	0.83[ASN][1000 genomes]
rs1641457	0.83[ASN][1000 genomes]
rs1641458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1651355	0.83[ASN][1000 genomes]
rs28628343	0.90[ASN][1000 genomes]
rs35487690	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366578	1.00[JPT][hapmap]
rs368642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs369140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs371909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs372052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs373602	0.88[ASN][1000 genomes]
rs373606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs374711	0.84[ASN][1000 genomes]
rs3749056	1.00[JPT][hapmap]
rs375180	0.84[ASN][1000 genomes]
rs376170	0.83[ASN][1000 genomes]
rs379410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs380082	1.00[JPT][hapmap]
rs380975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs384511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs384791	0.83[ASN][1000 genomes]
rs384994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs385561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389992	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs391631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs391984	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs393711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs394112	1.00[JPT][hapmap]
rs394540	1.00[JPT][hapmap]
rs395404	0.82[JPT][hapmap]
rs399061	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs401815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs402307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs405884	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs406222	1.00[JPT][hapmap]
rs406880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs407267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs407388	1.00[JPT][hapmap]
rs408009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs408662	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs410480	0.81[ASN][1000 genomes]
rs413711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs415695	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs417464	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs417591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs417873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs418380	0.83[ASN][1000 genomes]
rs418780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs421870	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs422411	0.81[ASN][1000 genomes]
rs423075	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs426295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs427632	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs428738	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs430314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap]
rs434082	1.00[JPT][hapmap]
rs434326	0.83[ASN][1000 genomes]
rs436010	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs439960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs440155	1.00[JPT][hapmap]
rs441196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs441413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs441802	0.80[ASN][1000 genomes]
rs442586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs443236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs450116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs450823	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs451074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451158	1.00[JPT][hapmap]
rs451811	1.00[JPT][hapmap]
rs452138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs505473	1.00[JPT][hapmap]
rs581477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs581568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs615449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs666362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs678107	1.00[JPT][hapmap]
rs679339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs688673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:60 , 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	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
4	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
5	chr2:40376800-40394200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:40379200-40393400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:40381800-40395200	Weak transcription	Spleen	Spleen
10	chr2:40382400-40392800	Strong transcription	Dnd41	blood
11	chr2:40386000-40395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:40386000-40395200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:40386400-40395200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:40387200-40392800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr2:40388400-40396400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:40388600-40395200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:40389400-40396200	Weak transcription	Placenta	Placenta
18	chr2:40389600-40393000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:40390600-40395200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:40390800-40395200	Weak transcription	Fetal Intestine Small	intestine
21	chr2:40391400-40393400	Enhancers	Fetal Muscle Leg	muscle
22	chr2:40391600-40393400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:40391600-40397600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:40391800-40392800	Genic enhancers	Fetal Heart	heart
25	chr2:40391800-40393200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:40391800-40393200	Enhancers	Ovary	ovary
27	chr2:40391800-40393400	Enhancers	Fetal Lung	lung
28	chr2:40391800-40393400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:40391800-40393400	Enhancers	NHDF-Ad	bronchial
30	chr2:40391800-40393600	Enhancers	Right Ventricle	heart
31	chr2:40392000-40393000	Enhancers	Esophagus	oesophagus
32	chr2:40392000-40393600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:40392000-40393600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:40392000-40393600	Enhancers	Gastric	stomach
35	chr2:40392000-40393600	Enhancers	Left Ventricle	heart
36	chr2:40392000-40393600	Enhancers	Right Atrium	heart
37	chr2:40392000-40393800	Enhancers	Rectal Smooth Muscle	rectum
38	chr2:40392000-40394200	Enhancers	Colon Smooth Muscle	Colon
39	chr2:40392000-40395200	Weak transcription	Small Intestine	intestine
40	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
41	chr2:40392200-40393000	Enhancers	Fetal Kidney	kidney
42	chr2:40392200-40393000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr2:40392200-40393200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr2:40392200-40393200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:40392200-40393200	Enhancers	NHLF	lung
46	chr2:40392200-40393400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:40392200-40393400	Enhancers	Aorta	Aorta
48	chr2:40392200-40393400	Enhancers	Lung	lung
49	chr2:40392200-40393400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr2:40392200-40393600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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