Variant report

Variant	rs41308086
Chromosome Location	chr20:1436445-1436446
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1436244..1441221-chr20:1444525..1448562,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11696447	0.85[AFR][1000 genomes];0.91[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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873522	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58194712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	0.95[AFR][1000 genomes];0.95[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	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66497853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124855	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs959813	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	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
3	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
4	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1419200-1443400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr20:1419600-1442000	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr20:1419800-1443600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr20:1420200-1437200	Strong transcription	Rectal Smooth Muscle	rectum
5	chr20:1420200-1444000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr20:1420200-1445600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr20:1420400-1443600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr20:1420400-1444600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr20:1420400-1444800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:1420400-1445800	Strong transcription	A549	lung
11	chr20:1420600-1444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:1421200-1444400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr20:1421400-1445200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:1421400-1446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:1421600-1444200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr20:1421600-1445800	Strong transcription	Placenta	Placenta
17	chr20:1421800-1437000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr20:1421800-1439400	Strong transcription	HMEC	breast
19	chr20:1421800-1442600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr20:1421800-1445800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr20:1422000-1437200	Strong transcription	NHLF	lung
22	chr20:1422000-1444800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr20:1422400-1440000	Strong transcription	GM12878-XiMat	blood
24	chr20:1422400-1442400	Strong transcription	Colonic Mucosa	Colon
25	chr20:1422400-1442600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr20:1422400-1444800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr20:1422600-1441600	Strong transcription	NHDF-Ad	bronchial
28	chr20:1422600-1442000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr20:1422600-1444200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr20:1422800-1442800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr20:1422800-1444800	Strong transcription	HUVEC	blood vessel
32	chr20:1423000-1443800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:1423200-1444600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr20:1423400-1441800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr20:1424200-1441400	Strong transcription	Colon Smooth Muscle	Colon
36	chr20:1424800-1437200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr20:1428800-1439600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr20:1428800-1440600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
39	chr20:1429200-1442000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr20:1430600-1436600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:1431000-1439800	Strong transcription	K562	blood
42	chr20:1431400-1437200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr20:1431600-1437400	Strong transcription	Gastric	stomach
44	chr20:1431600-1446400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr20:1432200-1436600	Strong transcription	Right Ventricle	heart
46	chr20:1432400-1437400	Strong transcription	Pancreas	Pancrea
47	chr20:1432400-1444000	Strong transcription	Left Ventricle	heart
48	chr20:1432400-1444400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr20:1432600-1436800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr20:1432600-1437000	Strong transcription	Aorta	Aorta

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