Variant report

Variant	rs60460559
Chromosome Location	chr4:16210349-16210350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:16209849..16215808-chr4:16226595..16229936,7	MCF-7	breast:
2	chr4:16207822..16210788-chr4:16227616..16230389,3	MCF-7	breast:
3	chr4:16207543..16210716-chr4:16226514..16229225,4	K562	blood:
4	chr4:16210098..16212174-chr4:16220610..16223093,2	K562	blood:
5	chr4:16206563..16211517-chr4:16224602..16229225,6	K562	blood:
6	chr4:16208663..16211668-chr4:16215718..16220403,4	K562	blood:

Variant related genes	Relation type
ENSG00000169762	Chromatin interaction
ENSG00000263327	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10516298	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10939653	0.81[ASN][1000 genomes]
rs11724076	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724423	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724467	0.82[ASN][1000 genomes]
rs11731602	0.86[ASN][1000 genomes]
rs11736424	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504884	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506249	0.81[ASN][1000 genomes]
rs12506478	0.96[ASN][1000 genomes]
rs12513244	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12643544	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645055	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651110	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373112	0.81[ASN][1000 genomes]
rs1662652	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16893099	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16893119	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16893138	0.86[ASN][1000 genomes]
rs16893143	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16893144	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16893147	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16893158	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28645901	0.82[ASN][1000 genomes]
rs35851218	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023844	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56218994	0.86[ASN][1000 genomes]
rs57089965	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58047733	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60768295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73128422	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73128457	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73130433	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130439	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130445	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73130451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73130453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73130456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657191	0.84[ASN][1000 genomes]
rs894639	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16168000-16213800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
3	chr4:16193000-16216000	Weak transcription	Spleen	Spleen
4	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
5	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
6	chr4:16193400-16211200	Weak transcription	Placenta	Placenta
7	chr4:16198600-16211200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:16198600-16216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:16198800-16211400	Weak transcription	Aorta	Aorta
12	chr4:16198800-16218800	Weak transcription	HSMM	muscle
13	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:16198800-16226000	Weak transcription	NHEK	skin
15	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:16199800-16215800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:16200000-16214200	Weak transcription	Fetal Heart	heart
18	chr4:16200800-16213600	Weak transcription	HUVEC	blood vessel
19	chr4:16200800-16214800	Weak transcription	Stomach Mucosa	stomach
20	chr4:16200800-16218000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:16203800-16211200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:16204200-16213800	Weak transcription	Ovary	ovary
24	chr4:16204600-16210400	Enhancers	Brain Angular Gyrus	brain
25	chr4:16204800-16210800	Enhancers	Brain Hippocampus Middle	brain
26	chr4:16204800-16226600	Weak transcription	NH-A	brain
27	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:16205800-16211600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:16206000-16211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:16206000-16211600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:16206400-16216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:16206400-16218400	Weak transcription	Fetal Lung	lung
33	chr4:16206600-16218400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:16207400-16210600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:16207400-16216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:16207600-16210400	Enhancers	Brain Germinal Matrix	brain
38	chr4:16208000-16210400	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr4:16208000-16210600	Weak transcription	HepG2	liver
40	chr4:16208200-16210400	Weak transcription	Thymus	Thymus
41	chr4:16208200-16211200	Weak transcription	K562	blood
42	chr4:16208200-16211400	Weak transcription	A549	lung
43	chr4:16208400-16210800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:16208400-16214400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:16208400-16214800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:16208400-16219000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
49	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:16208800-16210400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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