Variant report

Variant	rs6109848
Chromosome Location	chr20:13366426-13366427
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12106004	0.87[TSI][hapmap]
rs1812562	0.86[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28867078	0.83[EUR][1000 genomes]
rs45489891	0.96[EUR][1000 genomes]
rs45602236	0.96[EUR][1000 genomes]
rs55940819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6033689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6033690	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6033718	0.82[CEU][hapmap]
rs6042061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042063	0.86[ASW][hapmap];0.82[CEU][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042068	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042069	0.82[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042076	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042080	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6042093	0.82[CEU][hapmap]
rs6042105	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6042108	0.82[CEU][hapmap]
rs6042111	0.82[CEU][hapmap]
rs6042130	0.82[CEU][hapmap]
rs6042136	0.82[CEU][hapmap]
rs6042143	0.89[AMR][1000 genomes]
rs6042145	1.00[CEU][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs6042151	0.96[EUR][1000 genomes]
rs6042154	0.82[CEU][hapmap]
rs6105082	0.82[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6105083	0.86[ASW][hapmap];0.82[CEU][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6105091	0.82[CEU][hapmap]
rs6105097	0.82[CEU][hapmap]
rs6105108	0.82[CEU][hapmap]
rs6105109	0.82[CEU][hapmap]
rs6109849	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6109850	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6109868	0.82[CEU][hapmap]
rs6109872	0.81[MKK][hapmap]
rs6109882	0.96[EUR][1000 genomes]
rs6109883	0.82[CEU][hapmap]
rs6109885	0.82[CEU][hapmap]
rs6109889	0.82[CEU][hapmap]
rs6109895	1.00[CEU][hapmap]
rs6109896	1.00[CEU][hapmap]
rs6109901	0.82[CEU][hapmap]
rs7274078	0.82[CEU][hapmap]
rs8121784	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9653627	0.82[CEU][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	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13360200-13368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:13361800-13369400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr20:13362400-13368200	Weak transcription	Primary B cells from cord blood	blood
4	chr20:13362400-13370600	Weak transcription	HepG2	liver
5	chr20:13362600-13374000	Weak transcription	Fetal Lung	lung
6	chr20:13362600-13376800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:13362800-13368000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:13362800-13368200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr20:13362800-13368400	Weak transcription	A549	lung
10	chr20:13362800-13368400	Weak transcription	NHEK	skin
11	chr20:13362800-13380600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:13363200-13377400	Weak transcription	Fetal Brain Female	brain
13	chr20:13363400-13373200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr20:13363600-13366600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:13363600-13366600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:13363600-13366800	ZNF genes & repeats	Aorta	Aorta
17	chr20:13363600-13375800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:13363600-13375800	Weak transcription	HSMMtube	muscle
19	chr20:13363800-13368000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:13363800-13368800	Weak transcription	Fetal Kidney	kidney
21	chr20:13363800-13373400	Weak transcription	Liver	Liver
22	chr20:13363800-13376200	Weak transcription	Fetal Muscle Leg	muscle
23	chr20:13364000-13368000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr20:13364000-13368200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr20:13364000-13377400	Weak transcription	Brain Angular Gyrus	brain
26	chr20:13364200-13368400	Weak transcription	HMEC	breast
27	chr20:13364400-13368600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr20:13364400-13370800	Weak transcription	Fetal Intestine Small	intestine
29	chr20:13364400-13371000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr20:13364400-13376400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
32	chr20:13364600-13367600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:13364600-13368200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr20:13364600-13368200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr20:13364600-13368600	Strong transcription	Dnd41	blood
36	chr20:13364600-13371800	Strong transcription	Primary T cells from cord blood	blood
37	chr20:13364600-13374200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr20:13364600-13379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr20:13364800-13368400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr20:13364800-13375400	Weak transcription	Colonic Mucosa	Colon
42	chr20:13364800-13377600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr20:13365200-13367600	Weak transcription	Fetal Thymus	thymus
44	chr20:13365400-13366600	Strong transcription	Thymus	Thymus
45	chr20:13365400-13367400	Strong transcription	Pancreas	Pancrea
46	chr20:13365400-13368400	Weak transcription	GM12878-XiMat	blood
47	chr20:13365400-13373000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr20:13365400-13375800	Weak transcription	HSMM	muscle
49	chr20:13365600-13367600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr20:13365600-13368200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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