Variant report

Variant	rs60065407
Chromosome Location	chr3:50048808-50048809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12107362	1.00[AMR][1000 genomes]
rs12107386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050905	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050918	0.81[AFR][1000 genomes]
rs17050921	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050924	1.00[AMR][1000 genomes]
rs17849464	1.00[AMR][1000 genomes]
rs2229648	1.00[AMR][1000 genomes]
rs28424211	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55750059	1.00[AMR][1000 genomes]
rs55913179	1.00[AMR][1000 genomes]
rs56263643	1.00[AMR][1000 genomes]
rs56297242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57347154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58095278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58363428	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58688714	1.00[AMR][1000 genomes]
rs59822920	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60234882	1.00[AMR][1000 genomes]
rs60844685	1.00[AMR][1000 genomes]
rs61156427	0.89[AFR][1000 genomes]
rs61435065	1.00[AMR][1000 genomes]
rs73832783	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832801	1.00[AMR][1000 genomes]
rs73834118	1.00[AMR][1000 genomes]
rs73834119	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834120	1.00[AMR][1000 genomes]
rs73834125	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834127	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835208	1.00[AMR][1000 genomes]
rs73835216	1.00[AMR][1000 genomes]
rs73835217	1.00[AMR][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	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
6	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:50010800-50087000	Weak transcription	NHLF	lung
8	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
9	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
11	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:50028000-50056400	Weak transcription	Ovary	ovary
14	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
15	chr3:50029800-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
17	chr3:50033800-50051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
19	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
20	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
21	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:50037600-50049200	Weak transcription	Brain Germinal Matrix	brain
23	chr3:50037600-50055400	Weak transcription	Hela-S3	cervix
24	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
25	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:50038800-50056800	Weak transcription	HepG2	liver
28	chr3:50039400-50050200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:50039400-50061800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:50039600-50050400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:50040400-50056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:50041200-50051600	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:50041400-50053400	Weak transcription	Fetal Lung	lung
35	chr3:50041400-50057000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:50041600-50050400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:50041600-50051000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:50041600-50053400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:50041600-50055200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:50041600-50056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:50041600-50057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:50041600-50058200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:50041600-50061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:50041600-50063000	Weak transcription	Brain Substantia Nigra	brain
46	chr3:50041600-50065200	Weak transcription	NH-A	brain
47	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
48	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain

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