Variant report

Variant	rs57592998
Chromosome Location	chr5:118838978-118838979
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	chr5:118831350..118835449-chr5:118835713..118839843,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11948865	1.00[EUR][1000 genomes]
rs11949545	1.00[EUR][1000 genomes]
rs11951660	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952687	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11955089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11956487	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11959643	1.00[EUR][1000 genomes]
rs11959779	1.00[EUR][1000 genomes]
rs12714	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1428437	1.00[EUR][1000 genomes]
rs2560723	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28943589	1.00[AMR][1000 genomes]
rs28943594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35164142	1.00[AMR][1000 genomes]
rs35182344	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35764784	1.00[EUR][1000 genomes]
rs3843986	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4099736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57270573	1.00[EUR][1000 genomes]
rs57990091	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58527989	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59177585	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59940947	1.00[EUR][1000 genomes]
rs60069733	1.00[EUR][1000 genomes]
rs60684792	1.00[EUR][1000 genomes]
rs60871537	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61460721	1.00[EUR][1000 genomes]
rs61645108	1.00[EUR][1000 genomes]
rs68126620	0.80[AFR][1000 genomes]
rs6868057	1.00[EUR][1000 genomes]
rs72547236	1.00[AMR][1000 genomes]
rs73236713	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73236767	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236771	1.00[EUR][1000 genomes]
rs73237264	1.00[EUR][1000 genomes]
rs73238798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73240903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73241213	1.00[EUR][1000 genomes]
rs73241292	1.00[EUR][1000 genomes]
rs73243205	1.00[EUR][1000 genomes]
rs73246514	1.00[EUR][1000 genomes]
rs73246536	1.00[EUR][1000 genomes]
rs73249960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73249990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73250002	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73251677	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73256182	1.00[EUR][1000 genomes]
rs7708761	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7711431	1.00[EUR][1000 genomes]
rs7711926	1.00[EUR][1000 genomes]
rs7723718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:118794800-118861200	Weak transcription	HSMM	muscle
3	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:118805200-118839400	Weak transcription	NHEK	skin
5	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
6	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
7	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
8	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
9	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
11	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
13	chr5:118808000-118839600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
15	chr5:118811200-118839600	Weak transcription	Brain Germinal Matrix	brain
16	chr5:118812000-118846400	Weak transcription	NHLF	lung
17	chr5:118814000-118845000	Weak transcription	Gastric	stomach
18	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
19	chr5:118814800-118839400	Weak transcription	Right Ventricle	heart
20	chr5:118814800-118844800	Weak transcription	Lung	lung
21	chr5:118815400-118839000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:118815800-118839000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:118815800-118845400	Weak transcription	HMEC	breast
24	chr5:118816000-118844000	Weak transcription	Hela-S3	cervix
25	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:118816800-118839600	Strong transcription	Adipose Nuclei	Adipose
27	chr5:118817000-118846400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:118817200-118839600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:118818400-118839600	Weak transcription	Fetal Kidney	kidney
30	chr5:118819000-118839200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:118819600-118844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:118820000-118839000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:118820000-118839600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:118820200-118846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:118821000-118839600	Strong transcription	Liver	Liver
36	chr5:118821000-118843800	Weak transcription	NHDF-Ad	bronchial
37	chr5:118827600-118847800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:118828000-118840400	Weak transcription	Osteobl	bone
39	chr5:118829200-118840200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:118829600-118839600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr5:118829800-118844800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr5:118830400-118845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:118831000-118840200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:118832400-118839600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:118832400-118878200	Weak transcription	NH-A	brain
46	chr5:118832600-118844400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:118832600-118868600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr5:118832800-118843800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:118832800-118844600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:118833000-118839600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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