Variant report

Variant	rs6109986
Chromosome Location	chr20:1415456-1415457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1413774..1421620-chr20:1445657..1450800,12	K562	blood:
2	chr20:1406951..1409518-chr20:1413752..1415775,2	K562	blood:
3	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
4	chr20:1409886..1412172-chr20:1413671..1415589,2	K562	blood:
5	chr20:1405728..1407229-chr20:1414214..1416774,2	MCF-7	breast:
6	chr20:1414416..1417829-chr20:1445784..1450800,6	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11696447	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873522	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308086	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58194712	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109837	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66497853	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124855	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs959813	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	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
5	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
2	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
6	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
7	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
8	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
16	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
17	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
18	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:1411000-1419600	Weak transcription	Fetal Intestine Large	intestine
20	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
21	chr20:1411200-1420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
25	chr20:1412400-1419000	Weak transcription	Brain Hippocampus Middle	brain
26	chr20:1412800-1420200	Weak transcription	Ovary	ovary
27	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
28	chr20:1413800-1419200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr20:1413800-1420400	Weak transcription	Gastric	stomach
30	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
31	chr20:1414200-1415600	Strong transcription	A549	lung
32	chr20:1414200-1416000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr20:1414400-1416000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr20:1414400-1416200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr20:1414400-1416800	Enhancers	Primary hematopoietic stem cells	blood
36	chr20:1414400-1416800	Enhancers	Dnd41	blood
37	chr20:1414600-1415800	Weak transcription	Small Intestine	intestine
38	chr20:1414600-1415800	Enhancers	K562	blood
39	chr20:1414600-1416200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:1414600-1416200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr20:1414600-1416400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr20:1414600-1416400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr20:1414600-1416400	Enhancers	Fetal Thymus	thymus
44	chr20:1414600-1416800	Enhancers	Primary B cells from peripheral blood	blood
45	chr20:1414600-1416800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr20:1414600-1419600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr20:1414800-1416800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr20:1414800-1419000	Weak transcription	Fetal Stomach	stomach
49	chr20:1415000-1415800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr20:1415000-1416000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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