Variant report

Variant	rs28451189
Chromosome Location	chr3:160982518-160982519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160977228..160979405-chr3:160981086..160982720,3	MCF-7	breast:
2	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
3	chr3:160980180..160982518-chr3:161034107..161036039,2	MCF-7	breast:
4	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
5	chr3:160962502..160964176-chr3:160980145..160982760,2	MCF-7	breast:
6	chr3:160936882..160947576-chr3:160982516..160994324,28	MCF-7	breast:
7	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000240567	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1017799	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12486069	0.82[ASN][1000 genomes]
rs12489004	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12489125	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12490149	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12494725	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12496235	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13315320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13319558	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13319771	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16831850	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16831864	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16831882	0.82[ASN][1000 genomes]
rs16831942	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2306209	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28704960	0.82[ASN][1000 genomes]
rs28713364	0.97[AMR][1000 genomes]
rs3925722	0.85[AMR][1000 genomes]
rs4296611	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4352387	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4468992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4580574	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4635725	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57903480	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59567999	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59593286	0.83[AMR][1000 genomes]
rs59757775	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59776766	0.82[ASN][1000 genomes]
rs59867530	0.82[AMR][1000 genomes]
rs60121330	0.82[ASN][1000 genomes]
rs6441350	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441363	0.94[AMR][1000 genomes]
rs6441365	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6441372	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6441375	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6762064	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6771581	0.83[AMR][1000 genomes]
rs6774919	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6775446	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6775931	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6778186	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6782518	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6785714	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6787447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6788738	0.97[AMR][1000 genomes]
rs6790805	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6796168	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6801664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6805976	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73017340	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73026933	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73026967	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73026968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73026983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73026987	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73026989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73878309	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7615833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7615868	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7624791	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7626773	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7634299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7651924	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7652624	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9290070	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9290071	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9682249	0.85[AMR][1000 genomes]
rs9810351	0.82[ASN][1000 genomes]
rs9812574	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9818470	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9818835	0.82[ASN][1000 genomes]
rs9819793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9822705	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9822916	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9823424	0.82[ASN][1000 genomes]
rs9824535	0.82[ASN][1000 genomes]
rs9824805	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9826857	0.82[ASN][1000 genomes]
rs9830183	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9833270	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9834806	0.94[AMR][1000 genomes]
rs9835530	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9838945	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9841871	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9842290	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9847842	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9851699	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9855112	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9855572	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9856742	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9858907	0.82[ASN][1000 genomes]
rs9859641	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9860980	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9862867	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9871753	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9876077	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9877309	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9880536	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9884100	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9985364	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
3	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
4	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
5	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
6	chr3:160958600-160983600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:160966200-160983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
10	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:160970200-160983800	Weak transcription	NHLF	lung
12	chr3:160970400-160984200	Weak transcription	Hela-S3	cervix
13	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:160971000-160983600	Weak transcription	Thymus	Thymus
16	chr3:160971000-160984200	Weak transcription	Brain Anterior Caudate	brain
17	chr3:160971000-160987400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:160971000-160989000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:160971200-160984400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:160971200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:160971800-160993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:160972600-160984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:160973000-160984000	Weak transcription	Stomach Mucosa	stomach
32	chr3:160973200-160983800	Weak transcription	K562	blood
33	chr3:160973200-160984600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:160973200-160993200	Weak transcription	Gastric	stomach
35	chr3:160973400-160989000	Weak transcription	Fetal Thymus	thymus
36	chr3:160974000-160983000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:160974600-160990000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:160975400-160995800	Weak transcription	Fetal Intestine Large	intestine
39	chr3:160976400-160985400	Weak transcription	Fetal Lung	lung
40	chr3:160976400-160989400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:160976600-160982800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:160976600-160983400	Weak transcription	HUVEC	blood vessel
43	chr3:160976600-160983800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:160976600-160984200	Weak transcription	Brain Germinal Matrix	brain
45	chr3:160976600-160989200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:160976600-160995400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:160976800-160983600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:160976800-160991800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:160977200-160982600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:160978000-160984800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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