Variant report

Variant	rs60801542
Chromosome Location	chr3:160978788-160978789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160974756..160978821-chr3:160984556..160987132,3	MCF-7	breast:
2	chr3:160977228..160979405-chr3:160981086..160982720,3	MCF-7	breast:
3	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
4	chr3:160977409..160979546-chr3:160987399..160989130,2	MCF-7	breast:
5	chr3:160977550..160980456-chr3:160980555..160982387,2	K562	blood:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11539155	0.95[EUR][1000 genomes]
rs12108169	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12374001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629929	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12630038	0.95[AMR][1000 genomes]
rs12631467	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632346	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12633103	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636434	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12636590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450530	0.85[EUR][1000 genomes]
rs16834031	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1904204	0.95[AMR][1000 genomes]
rs28384383	0.95[EUR][1000 genomes]
rs28853731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4132373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55949838	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56174161	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56741879	0.95[AMR][1000 genomes]
rs56890199	0.89[AMR][1000 genomes]
rs57441646	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59827519	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60228180	0.95[AMR][1000 genomes]
rs60277631	0.94[AMR][1000 genomes]
rs61193379	0.95[AMR][1000 genomes]
rs61388164	0.83[AMR][1000 genomes]
rs61578814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61596736	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800515	0.85[EUR][1000 genomes]
rs73875453	0.83[AMR][1000 genomes]
rs73875455	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875456	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73875458	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73875460	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875464	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73875473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73875482	0.95[AMR][1000 genomes]
rs73875492	0.95[AMR][1000 genomes]
rs73875500	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73875502	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73878303	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73878304	0.90[EUR][1000 genomes]
rs73878305	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7652447	0.84[AMR][1000 genomes];0.90[EUR][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:105 , 50 per page) page: 1 2 3

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	chr3:160966200-160980800	Weak transcription	Fetal Stomach	stomach
8	chr3:160966200-160983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
11	chr3:160966400-160982000	Weak transcription	Fetal Intestine Small	intestine
12	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:160970200-160979000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:160970200-160980800	Weak transcription	NHEK	skin
15	chr3:160970200-160983800	Weak transcription	NHLF	lung
16	chr3:160970400-160980600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:160970400-160984200	Weak transcription	Hela-S3	cervix
18	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:160970800-160981800	Weak transcription	Lung	lung
20	chr3:160970800-160982200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:160971000-160981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:160971000-160981800	Weak transcription	Ovary	ovary
24	chr3:160971000-160982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:160971000-160983600	Weak transcription	Thymus	Thymus
26	chr3:160971000-160984200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:160971000-160987400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:160971000-160989000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:160971200-160982000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:160971200-160984400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:160971200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:160971400-160982000	Weak transcription	HepG2	liver
38	chr3:160971600-160982000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:160971800-160980800	Weak transcription	Left Ventricle	heart
40	chr3:160971800-160993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
42	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:160972600-160984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:160973000-160984000	Weak transcription	Stomach Mucosa	stomach
46	chr3:160973200-160980800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:160973200-160980800	Weak transcription	HSMMtube	muscle
48	chr3:160973200-160982000	Weak transcription	Aorta	Aorta
49	chr3:160973200-160983800	Weak transcription	K562	blood
50	chr3:160973200-160984600	Weak transcription	Primary T cells fromperipheralblood	blood

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