Variant report

Variant	rs6040471
Chromosome Location	chr20:11230127-11230128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JAG1-10	chr20:11230088-11230173	NONHSAT078624

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1473700	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473701	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473702	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473703	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015108	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076643	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076644	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076645	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076646	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076647	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2143857	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2143859	0.90[ASN][1000 genomes]
rs2179827	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2207098	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2207099	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2207100	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2223858	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327366	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327368	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876220	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876221	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4384859	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435520	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4449208	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632419	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4643605	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813966	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813967	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4813968	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813969	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813970	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813971	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813972	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813974	0.81[CHB][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs4813975	0.84[AMR][1000 genomes]
rs6033062	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6033063	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6033066	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033067	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6033068	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033069	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033070	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033071	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033072	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040435	0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs6040436	0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs6040442	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6040446	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040447	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040450	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040451	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040452	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040456	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6040458	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040459	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040460	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040461	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040463	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040464	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040465	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040466	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040469	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6040470	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6040472	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040473	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040475	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040477	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6040479	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040480	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040481	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040482	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6040486	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6040487	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6040489	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6040490	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6078105	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6078109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6104726	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6108870	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6108871	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6108872	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6108876	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6108882	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714690	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs714691	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs714692	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs761471	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs761472	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs926725	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs983251	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983252	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983342	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983343	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv585415	chr20:11134907-11383327	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11216200-11238800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11225400-11231000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr20:11227000-11230800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:11227400-11235000	Weak transcription	Fetal Kidney	kidney
5	chr20:11228200-11230600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr20:11228200-11230800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr20:11228800-11230200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:11228800-11230200	Enhancers	Fetal Brain Male	brain
9	chr20:11228800-11230400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr20:11228800-11230800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr20:11229000-11230400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr20:11229000-11230600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:11229200-11230200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr20:11229200-11230200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr20:11229200-11230800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr20:11229200-11230800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr20:11229400-11230200	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr20:11229400-11230600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr20:11229400-11230600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr20:11229600-11230200	Active TSS	Brain Angular Gyrus	brain
21	chr20:11229600-11230200	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr20:11229600-11230200	Flanking Active TSS	Fetal Brain Female	brain
23	chr20:11229600-11230200	Bivalent Enhancer	NH-A	brain
24	chr20:11229600-11230400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:11229600-11230400	Active TSS	Brain Anterior Caudate	brain
26	chr20:11229600-11230800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr20:11229800-11230200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr20:11229800-11230200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr20:11229800-11230200	Enhancers	Primary hematopoietic stem cells	blood
30	chr20:11229800-11230200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr20:11229800-11230200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr20:11229800-11230200	Active TSS	Brain Hippocampus Middle	brain
33	chr20:11229800-11230200	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr20:11229800-11230200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr20:11229800-11230200	Flanking Active TSS	Osteobl	bone
36	chr20:11229800-11230400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:11230000-11230200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr20:11230000-11230200	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr20:11230000-11230400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr20:11230000-11230800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr20:11230000-11231000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:11230000-11231000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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