Variant report

Variant	rs430473
Chromosome Location	chr2:40428263-40428264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40427590..40429513-chr2:40436431..40438074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227028	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs105288	0.89[ASN][1000 genomes]
rs118899	0.87[ASN][1000 genomes]
rs1641452	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1641456	0.95[ASN][1000 genomes]
rs1641457	0.95[ASN][1000 genomes]
rs1641458	0.95[ASN][1000 genomes]
rs1651355	0.95[ASN][1000 genomes]
rs28628343	0.84[ASN][1000 genomes]
rs36162999	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36184451	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs368642	0.96[ASN][1000 genomes]
rs369140	0.95[ASN][1000 genomes]
rs372052	0.95[ASN][1000 genomes]
rs373602	0.89[ASN][1000 genomes]
rs373606	0.82[ASN][1000 genomes]
rs374159	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs374711	0.96[ASN][1000 genomes]
rs375180	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs376170	0.95[ASN][1000 genomes]
rs376491	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs379410	0.93[ASN][1000 genomes]
rs379859	0.80[AMR][1000 genomes]
rs380082	0.84[EUR][1000 genomes]
rs380975	0.95[ASN][1000 genomes]
rs383073	0.80[AMR][1000 genomes]
rs384511	0.92[ASN][1000 genomes]
rs384791	0.95[ASN][1000 genomes]
rs384994	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs385561	0.95[ASN][1000 genomes]
rs389109	0.95[ASN][1000 genomes]
rs389992	0.81[EUR][1000 genomes]
rs391631	0.92[ASN][1000 genomes]
rs393711	0.95[ASN][1000 genomes]
rs394112	0.82[EUR][1000 genomes]
rs399061	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs401815	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs402307	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs406736	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs406880	0.87[ASN][1000 genomes]
rs407267	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs407388	0.82[EUR][1000 genomes]
rs408009	0.89[ASN][1000 genomes]
rs408662	0.93[ASN][1000 genomes]
rs410031	0.91[ASN][1000 genomes]
rs410480	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs413711	0.91[ASN][1000 genomes]
rs414766	0.91[ASN][1000 genomes]
rs417464	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs417591	0.88[ASN][1000 genomes]
rs417873	0.96[ASN][1000 genomes]
rs418380	0.95[ASN][1000 genomes]
rs418780	0.87[ASN][1000 genomes]
rs421870	0.87[ASN][1000 genomes]
rs422411	0.92[ASN][1000 genomes]
rs423075	0.96[ASN][1000 genomes]
rs426295	0.95[ASN][1000 genomes]
rs427632	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs429227	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs430314	0.92[ASN][1000 genomes]
rs430394	0.85[ASN][1000 genomes]
rs432142	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs432981	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs434326	0.95[ASN][1000 genomes]
rs436010	0.82[EUR][1000 genomes]
rs439960	0.96[ASN][1000 genomes]
rs440155	0.84[EUR][1000 genomes]
rs441196	0.88[ASN][1000 genomes]
rs441413	0.85[ASN][1000 genomes]
rs441593	0.88[ASN][1000 genomes]
rs441802	0.97[ASN][1000 genomes]
rs442476	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs444504	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs450116	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs450823	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs451074	0.87[ASN][1000 genomes]
rs452138	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs479909	0.85[ASN][1000 genomes]
rs4952596	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs581477	0.91[ASN][1000 genomes]
rs581568	0.91[ASN][1000 genomes]
rs666362	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs678107	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs679339	0.96[ASN][1000 genomes]
rs688673	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
10	esv2763455	chr2:40416373-40433420	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1001866	chr2:40416373-40433420	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv581503	chr2:40417012-40430611	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv581504	chr2:40418386-40430611	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv526425	chr2:40418386-40447587	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv526074	chr2:40423454-40451724	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40405400-40430000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:40417200-40430400	Weak transcription	Aorta	Aorta
3	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:40418600-40445800	Weak transcription	Dnd41	blood
5	chr2:40419200-40436600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:40420600-40430000	Weak transcription	NHLF	lung
7	chr2:40420800-40428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:40421200-40429200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:40422000-40435200	Weak transcription	Fetal Kidney	kidney
10	chr2:40422200-40430000	Weak transcription	Left Ventricle	heart
11	chr2:40422600-40436400	Weak transcription	Right Ventricle	heart
12	chr2:40424600-40430000	Weak transcription	Fetal Brain Male	brain
13	chr2:40424600-40430400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:40424800-40429800	Weak transcription	Fetal Brain Female	brain
15	chr2:40425200-40430000	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:40425400-40433400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:40426400-40430800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:40426600-40429000	Weak transcription	Fetal Stomach	stomach
19	chr2:40426600-40430000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:40426800-40429200	Genic enhancers	HSMM	muscle
21	chr2:40426800-40430800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:40427000-40429200	Enhancers	NHDF-Ad	bronchial
23	chr2:40427000-40431600	Enhancers	Fetal Heart	heart
24	chr2:40427800-40428600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40427800-40428800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:40427800-40428800	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:40427800-40429800	Weak transcription	HSMMtube	muscle
28	chr2:40427800-40429800	Weak transcription	Osteobl	bone
29	chr2:40428000-40429200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:40428000-40429800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:40428000-40430000	Weak transcription	Ovary	ovary

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