Variant report

Variant	rs1884390
Chromosome Location	chr20:1410818-1410819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1409886..1412172-chr20:1413671..1415589,2	K562	blood:
2	chr20:1408022..1413976-chr20:1445856..1450713,7	K562	blood:
3	chr20:1408581..1410916-chr20:1448637..1451105,2	K562	blood:
4	chr20:1408801..1411564-chr20:1423013..1426503,3	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap]
rs11696447	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap]
rs11699494	1.00[CHB][hapmap]
rs12481707	1.00[JPT][hapmap]
rs13163	1.00[CHB][hapmap]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793360	1.00[JPT][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884393	1.00[JPT][hapmap]
rs2064645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2273321	1.00[JPT][hapmap]
rs2873522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829697	1.00[JPT][hapmap]
rs41308086	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs58194712	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap]
rs6042506	1.00[CHB][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap]
rs6042574	1.00[CHB][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap]
rs6109511	1.00[CHB][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109837	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110189	1.00[CHB][hapmap]
rs6110193	1.00[CHB][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap]
rs66497853	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap]
rs8117563	1.00[CHB][hapmap]
rs8118276	1.00[CHB][hapmap]
rs8118710	1.00[JPT][hapmap]
rs8124855	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]
rs959813	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984497	1.00[JPT][hapmap]
rs984498	1.00[JPT][hapmap]

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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
3	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
4	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
5	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
9	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
10	chr20:1408400-1411000	Enhancers	K562	blood
11	chr20:1408600-1414400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
13	chr20:1408800-1414200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:1408800-1414400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:1408800-1415000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr20:1409000-1411200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr20:1409000-1411200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:1409000-1411400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
27	chr20:1409600-1413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr20:1409800-1411000	Enhancers	NHEK	skin
29	chr20:1409800-1411200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr20:1410000-1411000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:1410000-1411000	Enhancers	Fetal Intestine Large	intestine
32	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
33	chr20:1410200-1415000	Weak transcription	HMEC	breast
34	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
35	chr20:1410400-1411400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr20:1410400-1412000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr20:1410400-1412000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr20:1410600-1411000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr20:1410600-1411000	Enhancers	Adipose Nuclei	Adipose
41	chr20:1410600-1411400	Enhancers	Osteobl	bone
42	chr20:1410600-1411600	Enhancers	NHDF-Ad	bronchial
43	chr20:1410800-1411000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:1410800-1411000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr20:1410800-1411000	Enhancers	Psoas Muscle	Psoas
46	chr20:1410800-1411200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr20:1410800-1411200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr20:1410800-1411400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:1410800-1412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr20:1410800-1413200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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