Variant report

Variant	rs458829
Chromosome Location	chr5:70870158-70870159
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	chr5:70869939..70872632-chr5:70881848..70884470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10057258	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10079014	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1017225	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10942548	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12187886	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12652916	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13169095	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13182226	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13183892	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs156756	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs157192	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs157193	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs166758	0.86[AMR][1000 genomes]
rs16871757	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs169406	0.81[AMR][1000 genomes]
rs1990996	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059196	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs276589	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs277927	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277946	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277947	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277955	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs277977	0.85[AMR][1000 genomes]
rs277982	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277983	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277984	0.82[AMR][1000 genomes]
rs277987	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277988	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277989	0.81[AMR][1000 genomes]
rs277990	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277991	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277992	0.91[AMR][1000 genomes]
rs277993	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277994	0.86[AMR][1000 genomes]
rs277998	0.86[AMR][1000 genomes]
rs279289	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282357	0.86[AMR][1000 genomes]
rs368462	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3761966	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs388918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs411050	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs412766	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs421128	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs457889	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4602607	0.82[EUR][1000 genomes]
rs461942	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs462534	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs464639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs467880	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs467883	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468010	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs468796	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4703987	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4704050	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561139	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs617876	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67735897	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6872978	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs875136	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9885334	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3422117	chr5:70868025-70874173	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3328796	chr5:70868067-70873948	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70834000-70871800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:70846000-70872800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:70850000-70882200	Weak transcription	Psoas Muscle	Psoas
4	chr5:70856800-70882400	Weak transcription	NHEK	skin
5	chr5:70857000-70882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:70857800-70882200	Weak transcription	Brain Angular Gyrus	brain
7	chr5:70858600-70873800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:70858800-70882200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:70858800-70882200	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:70859200-70872400	Weak transcription	Ovary	ovary
11	chr5:70859200-70882400	Weak transcription	Right Ventricle	heart
12	chr5:70859400-70882200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:70861400-70882200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:70861400-70882400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:70861600-70882200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:70861600-70882200	Weak transcription	GM12878-XiMat	blood
17	chr5:70861600-70882400	Weak transcription	Primary B cells from cord blood	blood
18	chr5:70863200-70882400	Weak transcription	HUVEC	blood vessel
19	chr5:70864200-70882400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:70864200-70882400	Weak transcription	HSMM	muscle
21	chr5:70864400-70872400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:70864400-70873800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:70864400-70881800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:70864400-70882000	Weak transcription	Liver	Liver
25	chr5:70864400-70882200	Weak transcription	Left Ventricle	heart
26	chr5:70864400-70882200	Weak transcription	Pancreas	Pancrea
27	chr5:70864400-70882400	Weak transcription	HSMMtube	muscle
28	chr5:70864600-70870600	Weak transcription	NH-A	brain
29	chr5:70864600-70872600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:70864600-70873000	Weak transcription	Adipose Nuclei	Adipose
31	chr5:70864600-70873800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:70864600-70873800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:70864600-70873800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:70864600-70873800	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:70864600-70873800	Weak transcription	Lung	lung
36	chr5:70864600-70877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:70864600-70881800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr5:70864600-70882200	Weak transcription	Brain Anterior Caudate	brain
39	chr5:70864600-70882200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:70864600-70882200	Weak transcription	Brain Substantia Nigra	brain
41	chr5:70864600-70882200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:70864600-70882200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:70864600-70882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:70864600-70882400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:70864600-70882400	Weak transcription	Esophagus	oesophagus
46	chr5:70864600-70882400	Weak transcription	Fetal Intestine Large	intestine
47	chr5:70864600-70882400	Weak transcription	Thymus	Thymus
48	chr5:70864600-70882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:70864800-70873600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:70864800-70878200	Weak transcription	Brain Germinal Matrix	brain

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