Variant report

Variant	rs60014495
Chromosome Location	chr3:136237590-136237591
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136237342..136239151-chr3:136470510..136472888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10513016	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16843978	0.82[EUR][1000 genomes]
rs16844056	0.81[EUR][1000 genomes]
rs17266364	0.87[AMR][1000 genomes]
rs17365351	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17466223	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3931416	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763637	0.87[EUR][1000 genomes]
rs55848312	0.92[EUR][1000 genomes]
rs56083120	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095774	0.81[EUR][1000 genomes]
rs56218376	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681357	0.87[EUR][1000 genomes]
rs58636237	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58641485	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616231	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs59696368	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs60270684	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66470158	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs66471262	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs66494666	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66637228	0.82[EUR][1000 genomes]
rs66739346	0.82[EUR][1000 genomes]
rs66902780	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66973954	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67082054	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67230667	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67231188	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67236827	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67281610	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67303976	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67305360	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67621498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67663578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769582	0.80[EUR][1000 genomes]
rs6773495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773604	0.93[EUR][1000 genomes]
rs67794070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67888773	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67902591	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67971203	0.85[EUR][1000 genomes]
rs68018658	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72975363	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73224201	0.91[EUR][1000 genomes]
rs73226130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228025	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228037	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228040	0.89[EUR][1000 genomes]
rs7625592	0.85[EUR][1000 genomes]
rs7636806	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646563	0.82[EUR][1000 genomes]
rs7646723	0.82[EUR][1000 genomes]
rs923001	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60014495	IL20RB	cis	Nerve Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136240000	Weak transcription	HMEC	breast
3	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
5	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:136195400-136241800	Weak transcription	NH-A	brain
9	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:136212400-136249600	Weak transcription	Lung	lung
14	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
15	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:136213000-136251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:136213000-136252200	Weak transcription	Left Ventricle	heart
18	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:136213200-136246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:136213200-136246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:136214000-136239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:136214000-136246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:136214400-136238400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:136215600-136246200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:136220600-136240000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:136220600-136242800	Weak transcription	GM12878-XiMat	blood
27	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:136221000-136246400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:136221200-136241200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:136221200-136251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:136221400-136246400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:136221400-136251000	Weak transcription	Liver	Liver
33	chr3:136221600-136246200	Weak transcription	Fetal Intestine Large	intestine
34	chr3:136221600-136251000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:136222000-136246200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:136222000-136246600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:136222200-136238600	Weak transcription	Placenta	Placenta
38	chr3:136222200-136251000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:136222200-136251200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:136222400-136266200	Weak transcription	HSMM	muscle
41	chr3:136227800-136246600	Weak transcription	Fetal Thymus	thymus
42	chr3:136227800-136246600	Weak transcription	Thymus	Thymus
43	chr3:136230000-136246400	Weak transcription	Fetal Stomach	stomach
44	chr3:136230400-136251000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:136230600-136247600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:136230800-136246200	Weak transcription	Fetal Lung	lung
47	chr3:136232000-136241800	Weak transcription	Osteobl	bone
48	chr3:136232000-136263600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:136232200-136238200	Weak transcription	Psoas Muscle	Psoas
50	chr3:136232200-136246600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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